Solution to another Mac Pro sleep failure

I recently developed problems with my 2008 Mac Pro (3,1) failing to enter sleep modes. Attached displays no longer went to sleep, and hard disks would not spin down. After many hours of investigating this, I found that the Nalpeiron Protec6 software was the culprit. Never heard of it you say? Well I had not either. It is installed surreptitiously by a variety of software vendors as an anti-piracy mechanism. In my case it was installed by Nik Software's Viveza 2 installer; currently this installer does not tell you that they are installing another 3rd party application.
The Nalpeiron Protec6 software is installed in /Library/StartupItems/Protec6 folder. You can tell if the daemon software is running by typing ps ax | grep 'nalpeiron' in Terminal.app.
Renaming, changing load order, etc., didn't help. Viveza 2 won't run without it. So for now, goodbye Viveza and goodbye Protec6. Nuking the Protec6 folder and a quick restart seems to be all that's needed to rid your system of this garbage. Hope this is helpful

This problem is not just with Nik, but also onOne software. They both use Protec6 for their licensing and people have been experiencing these issues with either or (or both).
I have two solutions for you. Both come from the comments in this post:
http://trick77.com/2010/08/08/mac-doesnt-auto-sleep-anymore-hard-disks/
Solution 1: Some guy wrote an Applescript program that starts and stops the Protec6 service from running. So you can start it when you need it and then stop it so your computer can sleep. He has instructions and a download to the program in those comments.
Solution 2: Based on what someone says later in these comments, the newer update to Plug In Suite and Phototools fix this issue. Presumably bundled with a newer, bug free Protec6. I haven't tested this, but I bet if you install a demo version of the Plug In Suite or Phototools it will overwrite your Protec6 folder with the newer one and then Viveza will work as well and your computer will sleep again.

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    16.07.11 11:51:35          kernel          rooting via boot-uuid from /chosen: 43D7E44E-35C3-3C6B-8EEB-548E43D81587
    16.07.11 11:51:35          kernel          Waiting on <dict ID="0"><key>IOProviderClass</key><string ID="1">IOResources</string><key>IOResourceMatch</key><string ID="2">boot-uuid-media</string></dict>com.apple.AppleFSCompressionTypeZlib kmod start
    16.07.11 11:51:35          kernel          2.3.19 Little Snitch: starting
    16.07.11 11:51:35          kernel          com.apple.AppleFSCompressionTypeZlib load succeeded
    16.07.11 11:51:35          kernel          AppleIntelCPUPowerManagementClient: ready
    16.07.11 11:51:35          kernel          Intel82574L::staIrntt e-l 8B2u5i7l4tL ::sJtuanr t  7-  2B0u1i1l t1 6:J4u2n: 5 07  -2-0 1r1u n1n6i:n4g2 :o5n0  d-e-v ircuen naitn g on dev
    16.07.11 11:51:35          kernel          ice at
    16.07.11 11:51:35          kernel          BTCOEXIST off
    16.07.11 11:51:35          kernel          wl0: Broadcom BCM432b 802.11 Wireless Controller
    16.07.11 11:51:35          kernel          5.10.131.42
    16.07.11 11:51:35          kernel          FireWire (OHCI) TI ID 823f built-in now active, GUID 70cd60fffe6d31b6; max speed s800.
    16.07.11 11:51:35          kernel          Got boot device = IOService:/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI/SATA@1F,2/AppleAHCI/PRT2 @2/IOAHCIDevice@0/AppleAHCIDiskDriver/IOAHCIBlockStorageDevice/IOBlockStorageDri ver/WDC WD1001FALS-41Y6A0 Media/IOGUIDPartitionScheme/Customer@2
    16.07.11 11:51:35          kernel          BSD root: disk0s2, major 14, minor 2
    16.07.11 11:51:35          kernel          Kernel is LP64
    16.07.11 11:51:32          com.apple.launchd[1]          *** launchd[1] has started up. ***
    16.07.11 11:51:32          com.apple.launchd[1]          *** Verbose boot, will log to /dev/console. ***
    16.07.11 11:51:36          kernel          Intel82574L: Ethernet address 70:cd:60:a9:0a:c7
    16.07.11 11:51:36          kernel          Intel82574L: Ethernet address 70:cd:60:a8:f3:88
    16.07.11 11:51:36          kernel          AirPort_Brcm43224: Ethernet address c8:bc:c8:f4:bd:9dsystemShutdown false
    16.07.11 11:51:36          kernel          IO80211Controller::dataLinkLayerAttachComplete():  adding AppleEFINVRAM notification
    16.07.11 11:51:40          bootlog[44]          BOOT_TIME: 1310809891 0
    16.07.11 11:51:41          mDNSResponder[32]          mDNSResponder mDNSResponder-258.21 (May 26 2011 14:40:13) starting
    16.07.11 11:51:43          kernel          USBF:          11.997          AppleUSBHubPort: Port 2 of Hub at 0x5a100000 about to terminate a busy device (CompositeDevice) after waiting 10 seconds
    16.07.11 11:51:43          kernel          AirPort: Link Down on en2. Reason 1 (Unspecified).
    16.07.11 11:51:43          kernel          Previous Shutdown Cause: 0Waves SoundGrid Version: 2.0.0.14, Non-Interleaved Playback
    16.07.11 11:51:43          kernel          DSMOS has arrived
    16.07.11 11:51:43          kernel          ** Device in slot: SLOT-1 **
    16.07.11 11:51:43          kernel          00000000  ffffffff  Intel82574L::timeoutHandler - link is down
    16.07.11 11:51:44          kernel          Ethernet [Intel82574L]: Link up on en0, 100-Megabit, Full-duplex, Symmetric flow-control, Debug [796d,6f48,0de1,0200,45e1,4000]
    16.07.11 11:51:44          configd[13]          setting hostname to "Dominik-Rotherts-Mac-Pro.local"
    16.07.11 11:51:44          configd[13]          network configuration changed.
    16.07.11 11:51:44          blued[17]          Apple Bluetooth daemon started
    16.07.11 11:51:44          /System/Library/CoreServices/loginwindow.app/Contents/MacOS/loginwindow[33 ]          Login Window Application Started
    16.07.11 11:51:44          com.apple.SecurityServer[28]          Session 0x5fbff962 created
    16.07.11 11:51:45          com.apple.SecurityServer[28]          Entering service
    16.07.11 11:51:45          com.apple.kextd[10]          Can't load /System/Library/Extensions/MobileIODriver.kext - no code for running kernel's architecture.
    16.07.11 11:51:45          com.apple.kextd[10]          Failed to load /System/Library/Extensions/MobileIODriver.kext - (libkern/kext) requested architecture/executable not found.
    16.07.11 11:51:45          com.apple.kextd[10]          Load com.mhlabs.driver.MobileIOAudioDriver.10.5 failed; removing personalities.
    16.07.11 11:51:45          kernel          Starting: @(#)$Id: MobileIOAudioDevice.cpp 2298 2010-10-28 08:32:26Z bj $
    16.07.11 11:51:45          kernel          Build #: 5.4d208 [0704]
    16.07.11 11:51:45          kernel          Timing:-- Using Timers
    16.07.11 11:51:45          kernel          MobileIOAudioDevice[0xffffff80ff7fe000]::start(0xffffff8020ad9000)
    16.07.11 11:51:45          kernel          MobileIOAudioDevice[0xffffff80ff7fe000]::start(0xffffff8020ad9000) hwbt: 0 bt: 0 sn: 4000
    16.07.11 11:51:45          kernel          mCurrentClockSourceAddr: c036
    16.07.11 11:51:45          kernel          Firmware: 5.0.37
    16.07.11 11:51:45          kernel          2dCardType: 1
    16.07.11 11:51:45          kernel          fDoesntNeedInputChannelFlip: 1
    16.07.11 11:51:45          kernel          MobileIOAudioEngine[0xffffff8021549e00]::init()
    16.07.11 11:51:45          kernel          New Sample Offset: 18
    16.07.11 11:51:46          com.apple.kextd[10]          Can't load /System/Library/Extensions/IOSerialFamily.kext/Contents/PlugIns/InternalModemSu pport.kext - no code for running kernel's architecture.
    16.07.11 11:51:46          com.apple.kextd[10]          Failed to load /System/Library/Extensions/IOSerialFamily.kext/Contents/PlugIns/InternalModemSu pport.kext - (libkern/kext) requested architecture/executable not found.
    16.07.11 11:51:46          com.apple.kextd[10]          Load com.apple.driver.InternalModemSupport failed; removing personalities.
    16.07.11 11:51:47          kernel          AppleTyMCEDriver::start coreVIDPID = 0x2c708086 Number of packages = 1 Number of cpus = 16 memory monitor trough PCI
    16.07.11 11:51:47          configd[13]          network configuration changed.
    16.07.11 11:51:47          configd[13]          network configuration changed.
    16.07.11 11:51:47          com.apple.usbmuxd[24]          usbmuxd-211 built on Feb  8 2011 at 13:49:43 on Feb  8 2011 at 13:49:43, running 64 bit
    16.07.11 11:51:48          kernel          Auth result for: 00:0c:f6:55:a3:8c MAC AUTH succeeded
    16.07.11 11:51:48          kernel          AirPort: Link Up on en2
    16.07.11 11:51:49          kernel          AirPort: RSN handshake complete on en2
    16.07.11 11:51:52          AGProtocolService[49]          Waves SG Protocol Service: Could not Start Kernel Driver Streaming!
    16.07.11 11:51:54          configd[13]          network configuration changed.
    16.07.11 11:51:58          kernel          CompositeDevice::terminate(kIOServiceSynchronous) timeout
    16.07.11 11:52:02          configd[13]          network configuration changed.
    16.07.11 11:52:06          kernel          [ffffff8021553c00][BNBTrackpadDevice::init][54] init is complete
    16.07.11 11:52:06          kernel          [ffffff8021553c00][BNBTrackpadDevice::probe][54] entered
    16.07.11 11:52:07          kernel          [ffffff8021553c00][BNBTrackpadDevice::handleStart][54] Done
    16.07.11 11:52:07          kernel          [ffffff8022493a00][AppleMultitouchHIDEventDriver::start] entered
    16.07.11 11:52:07          kernel          [ffffff80224bbc00][AppleMultitouchDevice::start] entered
    16.07.11 11:52:35          configd[13]          InterfaceNamer: timed out waiting for IOKit to quiesce
    16.07.11 11:52:35          configd[13]          InterfaceNamer: Busy services :
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1 [1]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert [1]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert/PCI0@0 [1]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI [1]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI/UHC6@1A,2 [1]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI/UHC6@1A,2/AppleUSBUHCI [1]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI/UHC6@1A,2/AppleUSBUHCI/Co mpositeDevice@5a120000 [4]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI/UHC6@1A,2/AppleUSBUHCI/Co mpositeDevice@5a120000/IOUSBCompositeDriver [1]
    16.07.11 11:52:35          configd[13]          InterfaceNamer:   MacPro5,1/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI/UHC6@1A,2/AppleUSBUHCI/Co mpositeDevice@5a120000/IOUSBInterface@0 [2]
    16.07.11 11:52:48          WindowServer[65]          kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.
    16.07.11 11:52:48          com.apple.WindowServer[65]          Sat Jul 16 11:52:48 Dominik-Rotherts-Mac-Pro.local WindowServer[65] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.
    16.07.11 11:52:49          kernel          Sound assertion ""Graphics vendor supplied 'av-signal-type' property indicates a DVI device with audio capabilities has been attached but cannot be supported."" failed in AppleHDAController at line 2283 goto handler
    16.07.11 11:52:49          kernel          Sound assertion ""Graphics vendor supplied 'av-signal-type' property indicates a DVI device with audio capabilities has been attached but cannot be supported."" failed in AppleHDAController at line 2283 goto handler
    16.07.11 11:52:49          com.apple.SecurityServer[28]          Session 0x22edb7 created
    16.07.11 11:52:49          com.apple.SecurityServer[28]          Session 0x22edb7 attributes 0x30
    16.07.11 11:52:50          loginwindow[33]          Login Window Started Security Agent
    16.07.11 11:52:50          SecurityAgent[106]          User info context values set for Dominik
    16.07.11 11:52:50          SecurityAgent[106]          Login Window login proceeding
    16.07.11 11:52:50          SecurityAgent[106]          Login Window done
    16.07.11 11:52:50          loginwindow[33]          Login Window - Returned from Security Agent
    16.07.11 11:52:50          loginwindow[33]          USER_PROCESS: 33 console
    16.07.11 11:52:50          com.apple.loginwindow[33]          PING 169.254.100.231 (169.254.100.231): 56 data bytes
    16.07.11 11:52:50          com.apple.loginwindow[33]          64 bytes from 169.254.100.231: icmp_seq=0 ttl=255 time=0.081 ms
    16.07.11 11:52:50          com.apple.loginwindow[33]          --- 169.254.100.231 ping statistics ---
    16.07.11 11:52:50          com.apple.loginwindow[33]          1 packets transmitted, 1 packets received, 0.0% packet loss
    16.07.11 11:52:50          com.apple.loginwindow[33]          round-trip min/avg/max/stddev = 0.081/0.081/0.081/0.000 ms
    16.07.11 11:52:50          com.apple.launchctl.Aqua[112]          launchctl: Please convert the following to launchd: /etc/mach_init_per_user.d/com.adobe.SwitchBoard.monitor.plist
    16.07.11 11:52:50          com.apple.launchd.peruser.501[90]          (com.apple.ReportCrash) Falling back to default Mach exception handler. Could not find: com.apple.ReportCrash.Self
    16.07.11 11:52:51          com.apple.loginwindow[33]          route: writing to routing socket: No such process
    16.07.11 11:52:51          com.apple.loginwindow[33]          route: writing to routing socket: No such process
    16.07.11 11:52:51          com.apple.loginwindow[33]          route: writing to routing socket: No such process
    16.07.11 11:52:57          com.apple.launchd.peruser.501[90]          (com.apple.Kerberos.renew.plist[141]) Exited with exit code: 1
    16.07.11 11:52:57          com.apple.launchd.peruser.501[90]          (0x102300070.mach_init.switchboard.sh) Failed to check-in!
    16.07.11 11:52:58          com.apple.usbmuxd[24]          HandleUSBMuxDictionary client 0x101800490-iTunesHelper/com.apple.iTunesHelper using library usbmuxd-211 built on Jan 13 2011 at 04:19:31, running usbmuxd-211 built on Feb  8 2011 at 13:49:43
    16.07.11 11:53:04          MIDIServer[164]          MIDIServer [164] starting; arch=x86_64
    16.07.11 11:53:05          MIDIServer[164]          PlugIn EuphonixMIDI.plugin -- /Library/Audio/MIDI Drivers/ does not contain a supported architecture.
    16.07.11 11:53:05          MIDIServer[164]          MIDIServer relaunching because a 32-bit driver was found
    16.07.11 11:53:06          MIDIServer[164]          MIDIServer [164] starting; arch=i386
    16.07.11 11:53:06          EuControl[128]          CoreText: Invalid 'kern' Subtable In CTFont <name: MetaKorrespondenz-Bold, size: 26.000000, matrix: 0x0>
    CTFontDescriptor <attributes: <CFBasicHash 0x2510fc0 [0xa08e8ec0]>{type = mutable dict, count = 1,
    entries =>
              1 : <CFString 0xa05a3d78 [0xa08e8ec0]>{contents = "NSFontNameAttribute"} = <CFString 0x2607c90 [0xa08e8ec0]>{contents = "MetaKorrespondenz-Bold"}
    >
    16.07.11 11:53:06          EuControl[128]          EuControl finished launching...
    16.07.11 11:53:06          EuControl[128]          Starting EuCon...
    16.07.11 11:53:08          MIOConsole[155]          Open Succeeded
    16.07.11 11:53:08          MIOConsole[155]          Reg Session ref = 20ad7800 Session ref = 1; mIOService = 4503
    16.07.11 11:53:08          MIOConsole[155]          MIOAddMIOUnit: Box attached! [0] - 0x2010a00 - Mobile I/O 2882 s/n: 5
    16.07.11 11:53:09          [0x0-0x17017].com.Euphonix.EuConDiscovery[170]          Starting to discover, main tid:15745024
    16.07.11 11:53:48          kernel          npvhash=4095
    16.07.11 11:53:09          [0x0-0x17017].com.Euphonix.EuConDiscovery[170]          Successfully inited discovery ORB

    Okay, I just came a step further with troubleshooting but still hope someone may help me out of this.
    Everytime I shutdown the system before the error occurs again on bootup, the shutdown messages contain something like "AppleBluetooth ..." after unmounting all disks - unfortunately I cannot find this message in the logfiles but it's there on shutdown (using verbose mode) just before the system halts. Then, the next boot will lead to the mentioned problems. If I shutdown the system and the message does not appear, everything's going to be fine on bootup.
    There must be something wrong with the wireless keyboard + magic trackpad:
    Jul 17 20:21:08 localhost kernel[0]: USBF:          11.976          AppleUSBHubPort: Port 2 of Hub at 0x5a100000 about to terminate a busy device (CompositeDevice) after waiting 10 seconds
    Jul 17 20:21:16 Dominik-Rotherts-Mac-Pro kernel[0]: [ffffff8021462800][BNBTrackpadDevice::init][54] init is complete
    Jul 17 20:21:16 Dominik-Rotherts-Mac-Pro kernel[0]: [ffffff8021462800][BNBTrackpadDevice::probe][54] entered
    Jul 17 20:21:16 Dominik-Rotherts-Mac-Pro kernel[0]: 00000000  ffffffff  Intel82574L::timeoutHandler - link is down
    Jul 17 20:21:16 Dominik-Rotherts-Mac-Pro kernel[0]: [ffffff8021462800][BNBTrackpadDevice::handleStart][54] Done
    Jul 17 20:21:16 Dominik-Rotherts-Mac-Pro kernel[0]: [ffffff802223e000][AppleMultitouchHIDEventDriver::start] entered
    Jul 17 20:21:16 Dominik-Rotherts-Mac-Pro kernel[0]: [ffffff802231c100][AppleMultitouchDevice::start] entered
    Jul 17 20:21:23 Dominik-Rotherts-Mac-Pro kernel[0]: CompositeDevice::terminate(kIOServiceSynchronous) timeout

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