Right USB Port stops working after disconnecting device since 10.9.2

Question

Hi,
Since updating to 10.9.2 the right USB port on my MBA stops working after diconnecting a device (tested: external hard drive, USB flash drive, USB HSPA Modem). The only way to get the port recognizing the device on that port is to do a restart. If the device is connected from starting the MBA it works fine, if I then eject the drive and reinsert it or a different USB device the device doesn't get recognized. The devices do get power, my WD passport ultra spins up just fine, the USB HSPA modem also indicates it's working (with signal) but nothing shows up in finder or diskutility. If the modem is connected from start (and thus working) and then disconnect from the internet but not remove the drive I can reconnect to the internet. The problem only occurs after disconnecting the device. The port becomes inactive. The left USB port works as expected.
Steps I've taken:
Disk Persmission
PRAM
SMC
Reapplied the 10.9.2 update
Sent feedback to Apple
Some Output:
Boot Mode: Normal
Total CPU usage:
   User 11%                    System 10%
Max %CPU by process (name, UID, %):
   WindowServer         0   4.6
Loaded extrinsic kernel extensions:
   at.obdev.nke.LittleSnitch (4052)
   com.driver.JRDUSBModemData64 (4.0.5)
   com.protech.NoSleep (1.3.3)
Loaded extrinsic daemons:
   net.sourceforge.MonolingualHelper
   com.oracle.java.JavaUpdateHelper
   com.oracle.java.Helper-Tool
   com.microsoft.office.licensing.helper
   com.freemacsoft.appcleanerd
   com.adobe.fpsaud
   at.obdev.littlesnitchd
Loaded extrinsic user agents:
   com.oracle.java.Java-Updater
   at.obdev.LittleSnitchUIAgent
/Library/LaunchAgents:
   at.obdev.LittleSnitchUIAgent.plist
   com.oracle.java.Java-Updater.plist
/Library/LaunchDaemons:
   at.obdev.littlesnitchd.plist
   com.adobe.fpsaud.plist
   com.freemacsoft.appcleanerd.plist
   com.microsoft.office.licensing.helper.plist
   com.oracle.java.Helper-Tool.plist
   com.oracle.java.JavaUpdateHelper.plist
   net.sourceforge.MonolingualHelper.plist
/Library/PrivilegedHelperTools:
   com.freemacsoft.appcleanerd
   com.microsoft.office.licensing.helper
   com.oracle.java.JavaUpdateHelper
   net.sourceforge.MonolingualHelper
Extrinsic loadable bundles:
   /System/Library/Extensions/JRDMassStorageDriver32.kext
             (No bundle ID)
   /System/Library/Extensions/JRDMassStorageDriver64.kext
             (No bundle ID)
   /System/Library/Extensions/JRDUSBModemData32.kext
             (com.driver.JRDUSBModemData32)
   /System/Library/Extensions/JRDUSBModemData64.kext
             (com.driver.JRDUSBModemData64)
   /System/Library/Extensions/LittleSnitch.kext
             (at.obdev.nke.LittleSnitch)
   /System/Library/Extensions/NoSleep.kext
             (com.protech.NoSleep)
   /Library/Audio/Plug-Ins/Components/A52Codec.component
             (com.shepmater.A52Codec)
   /Library/Internet Plug-Ins/Flash Player.plugin
             (com.macromedia.Flash Player.plugin)
   /Library/Internet Plug-Ins/JavaAppletPlugin.plugin
             (com.oracle.java.JavaAppletPlugin)
   /Library/PreferencePanes/Flash Player.prefPane
             (com.adobe.flashplayerpreferences)
   /Library/PreferencePanes/JavaControlPanel.prefPane
             (com.oracle.java.JavaControlPanel)
   /Library/PreferencePanes/NoSleep.prefPane
             (com.protech.NoSleepPref)
   /Library/QuickTime/AC3MovieImport.component
             (com.cod3r.ac3movieimport)
   /Library/Spotlight/LogicPro.mdimporter
             (No bundle ID)
   Library/Address Book Plug-Ins/SkypeABDialer.bundle
             (com.skype.skypeabdialer)
   Library/Address Book Plug-Ins/SkypeABSMS.bundle
             (com.skype.skypeabsms)
   Library/QuickLook/Pacifist.qlgenerator
             (com.charlessoft.pacifist.qlgenerator)
   Library/Services/Clip to Day One.workflow
             (No bundle ID)
Login hook:
   /Library/Scripts/Hooks/login.sh
Global login items:
   $HELPER_PATH
   $HELPER_PATH
   $HELPER_PATH
   $HELPER_PATH
   $HELPER_PATH
User login items:
   iTunesHelper
   Sparrow
   Sort Menubar Items
   AppCleaner Helper
   SurplusMeterAgent
Safari extensions:
   Shut Up
   AdBlock
   SafariKeywordSearch
   Disconnect
   MapTricks
Restricted user files: 28
Font problems: 0
Elapsed time (s): 130
etrecheck output:
Hardware Information:
          MacBook Air - model: MacBookAir3,1
          1 1.4 GHz Intel Core 2 Duo CPU: 2 cores
          2 GB RAM
Video Information:
          NVIDIA GeForce 320M - VRAM: 256 MB
System Software:
          OS X 10.9.2 (13C64) - Uptime: 0 days 0:20
Disk Information:
          APPLE SSD TS064C disk0 : (60.67 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    disk0s2 (disk0s2) <not mounted>: 59.81 GB
                    Recovery HD (disk0s3) <not mounted>: 650 MB
USB Information:
          EFI (disk2s1) <not mounted>: 209.7 MB
          Radha (disk2s2) /Volumes/Radha: 1.81 TB (1.73 TB free)
          disk2s3 (disk2s3) <not mounted>: 189.89 GB
          Boot OS X (disk2s4) <not mounted>: 134.2 MB
FireWire Information:
Kernel Extensions:
          at.obdev.nke.LittleSnitch          Version: 4052
          com.driver.JRDUSBModemData64          Version: 4.0.5
          com.protech.NoSleep          Version: 1.3.3
Problem System Launch Daemons:
Problem System Launch Agents:
Launch Daemons:
                 [loaded]          at.obdev.littlesnitchd.plist
                 [loaded]          com.adobe.fpsaud.plist
                 [loaded]          com.freemacsoft.appcleanerd.plist
                 [loaded]          com.microsoft.office.licensing.helper.plist
                 [loaded]          com.oracle.java.JavaUpdateHelper.plist
                 [loaded]          net.sourceforge.MonolingualHelper.plist
Launch Agents:
                 [loaded]          at.obdev.LittleSnitchUIAgent.plist
User Launch Agents:
User Login Items:
          iTunesHelper
          Sparrow
          Sort Menubar Items
          AppCleaner Helper
          SurplusMeterAgent
3rd Party Preference Panes:
          Flash Player
          Java
          NoSleep
Internet Plug-ins:
          Default Browser.plugin
          Flash Player.plugin
          FlashPlayer-10.6.plugin
          JavaAppletPlugin.plugin
          QuickTime Plugin.plugin
User Internet Plug-ins:
Bad Fonts:
          None
Top Processes by CPU:
              12%          com.apple.WebKit.Networking
               6%          Safari
               4%          WindowServer
               3%          EtreCheck
               2%          hidd
               1%          Terminal
               1%          notifyd
               1%          opendirectoryd
               1%          com.apple.WebKit.WebContent
               0%          Dock
Top Processes by Memory:
          147 MB          Safari
          137 MB          com.apple.WebKit.WebContent
          49 MB          mds_stores
          29 MB          com.apple.WebKit.Networking
          27 MB          TextEdit
          23 MB          WindowServer
          20 MB          Disk
          20 MB          Sparrow
          20 MB          CVMCompiler
          18 MB          Finder
Nothing out of the ordinairy. Thanks for any help

Answer 1

It's an Apple Pro keyboard and mouse, the dongle is
plugged into the Mac and not the keyboard. The same
set-up is, and has been working on all our other
Macs.
The sleep issue sounds interesting- hum, maybe...
Is your keyboard plugged into one of the USB connections on an Apple monitor? If so, you may want to change that connection to one that is on the G5 itself. My monitor came with a warning note indicating that problems will likely occur if the keyboard is connected to the monitor.
I also had a problem with the automatic sleep function. After much trouble-shooting and a logic board replacement, it was concluded that coming out of the automatic sleep function with any USB device active would freeze the entire USB bus. After disabling automatic sleep in system preferences, I've had no freezing problems. My machine works fine with the manual sleep function in the Apple Menu.
AndyH