H87M-G43 and automatic boot issues

I have an H87M-G43 and for 4 weeks have been struggling to get a new clean Windows 8.1 UEFI build on the PC without odd automatic boot issues.
Here is the PC configuration:
CPU Intel Core i5-4440 3.1GHz
PSU Corsair CX430
DIMM1:
DIMM2: Corsair XMS3 DDR3 4GB CMX4GX3M1A1333C9
DIMM3:
DIMM4: Corsair XMS3 DDR3 4GB CMX4GX3M1A1333C9
SATA Port 1: SSD Samsung 840 EVO 120GB
SATA Port 2:
SATA Port 3: HDD Samsung 1TB SATA II
SATA Port 4: HDD Samsung 1TB SATA II
SATA Port 5: DVD Liteon IHAS124-14 24X
SATA Port 6:
JAUD1: Coolermaster 352 Series Case Front I/O Intel HD Audio connector
JUSB1: Coolermaster 352 Series Case Front I/O USB 2.0 connector
JUSB4: Coolermaster 352 Series Case Front I/O USB 3.0 connector
BIOS v1.6:
01. F6 Restore Defaults: Load Optimized Defaults
02. SATA Mode: [RAID Mode]
03. SATA3 Hot Plug: Enabled
04. SATA4 Hot Plug: Enabled
05. Initiate Graphics Adapter: IGD
06. Serial(COM) Port 0: Disabled
07. Parallel(LPT) Port: Disabled
08. Windows 8/8.1 Feature: Enabled
09. Resume From S3/S4/S5 by USB Device: Enabled
10. GO2BIOS: Enabled
SATA Port 3+4 RAID1 (Mirror)
Windows 8.1 UEFI installation
Install Windows Update:
1. Important Updates
2. Recommended Updates
3. Optional Updates
Install MSI Drivers/Software:
01. Intel Chipset Driver 9.4.0.1026
02. Intel SVGA Driver 10.18.10.3412
03. Realtek PCIE Network Drivers 8.23.11.26.2013
04. Intel RAID Driver 12.9.0.1001
05. Realtek HD Audio Drivers 6.0.1.7111
06. MSI Wallpaper
07. Intel AMT Driver 9.5.15.1730
08. Intel SBA 2.2.39.7991
09. Intel Smart Connect Technology 4.2.40.2418
10. Super Charger 1.2.020
I have not configured any of the Intel Management and Security, Small Business Advantage, Smart Connect software, just installed them.
The issues I get are:
1. JUSB1 connected and Resume From S3/S4/S5 by USB Device: Enabled in BIOS. When I shutdown the PC, it automatically boots 2-3 seconds later. If I set Resume From S3/S4/S5 by USB Device: Disabled or disconnect the JUSB1, the PC shutdown is fine.
2. Once the PC is shutdown OK, PC boots itself several hours later. Yesterday at 15:50pm PC was shutdown. At 21:18pm, PC automatically booted itself.
This is my first MSI and UEFI motherboard. What I would like is some advice on setting up the BIOS and the software to get sleep/hibernate working and no automatic boots.
I have contacted MSI regarding these issues, but they say they cannot reproduce them. I have subsequently googled these issues and of course, other MSI users are experiencing similar problems, but there are no obvious resolutions. Please can anyone help/advise?

Hi,
I have the MSI Z87-GD65 Gaming mobo and perhaps similar problem as discussed in this thread.
I wanted to be able to wake my PC from sleep mode via my USB connected mouse and keyboard. Therefore I went into BIOS and set the "Resume from S3/S4/S5 by USB Device" to "Enabled". And yes, now it is possible to wake my PC from sleep mode by just clicking any button on my keyboard or just moving my mouse a little bit. So far so good. BUT, another feature was also added which I did not want to have: By just clicking any button on my keyboard or moving my mouse a little bit the PC also started after I have "shut it down"! This could seem as the PC boot by itself but it does not, I have to move the mouse just a little bit (by accident for example when needing more space on my desk) or clicking a button on the keyboard. I THINK THE ROOT CAUSE TO THIS PROBLEM IS AS FOLLOWS: In BIOS, it says "Resume from S3/S4/S5 by USB Device". Instead it should only be "Resume from S3 by USB Device". S3 is the same as "Sleep" and S5 is the same as "Soft off" = PC shutdown. Do you understand what I mean? When I shut down my PC it is put into state “S5”. (NOTE: I have another PC with MSI Z77-GD65 and here it only says "Resume from S3 by USB Device" and no problem with any starting of that PC via USB device from a shutdown state, it only starts from the sleep state (=”S3”) as I want. How do I get rid of the "S5" state in BIOS for this USB wake up feature? (Btw "S4" is hibernate state which is not the same as a shutdown PC, therefore not causing this problem.)
ADDED No. 1: Please read msdn.microsoft.com/en-us/library/windows/desktop/aa373229(v=vs.85).aspx for explanation of the different system Power states I mention above.
ADDED No. 2: My Click BIOS version is 1.8 for Z87-GD65 with release date 2013-12-06. On a Youtube video I have seen that version 1.0 of this BIOS has Wake up "Resume from S3 by USB Device" and not ...S3/S4/S5...

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    10. When the OD Master is ready click on Overview and check that the LDAP and Keberos Realm reflect your server's hostname.
    11. Go back to Workgroup Manager and re-import users and groups.
    NOTE: passwords are not being exported. I do not know how to salvage user passwords. (Maybe passwords can be recovered by re-mporting an OD archive - comments welcome! ).
    12. Go to Server App and reset passwords and (not to forget) user homefolder locations, in particular if you want to login from a network account!
    If the home directory has not been defined you cannot login from a network account.
    13. You may now want to restore Profile Manager user profiles in Terminal. Issue the following commands:
    sudo serveradmin stop devicemgr
    sudo serveradmin start postgres
    sudo psql -U _postgres -d device_management -f $HOME/device_management.sql
    sudo serveradmin start devicemgr
    14. You can now switch back on your services, including Profile Manager.
    In Profile Manager you may have to configure Device Management. This creates a correct Code Signng Certicate.
    15. Check the certificate settings in Server App -> Hadware -> Settings-> SSL Certificates.
    16. Check that Apple Push Notifications are set.(you easily check if they are working later)
    17. You may want to re-boot OS Server from the clone now.
    18. After re-boot open Server App and check that your server is running well.
    19. Delete all profiles in System Preferences -> Profiles.
    19. Login to Profile Manager. You should have all users and profiles back. In my experience devices have to be re-enrolled before profiles can be pushed and/or devices be enrolled. You may just as well delete the displayed devices now.
    20. Grab one of your (portable) Macs that you want to enrol and go to (yourhostname)/mydevices and install the server's trust profile. The profile's name  should read "Trust Profile for...) and underneath in green font "Verified".
    21. Re-enrol that device. At this stage keep your finger's crossed and take a deep breath.
    22. If the device has been successfully enrolled you may at last want to test if pushing profiles really works. Login to Profile Manager as admin, select the newly enrolled device. Check that Automatic Push is enabled (-> Profile -> General). Create a harmless management profile such as defining the dock's position on the target machine. (Do not forget to click SAVE at the end - this is easily missed here). If all is well Profile Manager will display an active task (sending) and the dock's position on the target will have changed in a few seconds if you are on a LAN (Note: If sending seems to take forever: check on the server machine and/or on your router that the proper ports are open and that incoming data is not intercepted by Little Snitch or similar software).
    Note: if you intend to enrol an Apple iPhone you may first need to install the proper Apple Configuration software.
    Now enjoy Profile and Device Manager !
    Regards,
    Twistan

    HI
    1. In Action profiles, logon to system and recheck correcion are available in action definition as well in condition configuration and the schedule condition is also maintained. but the display is not coming(i.e in the worklist this action is not getting displayed).
    You can check the schedule condition for the action and match the status values...or try recreating the action with schedule condition again....for customer specific ....copy the standard aciton with ur zname and make a schedule condition and check the same.
    2, In suppport team of incident when i give individual processor it throwing a warning that u r not the processor. but when i give org unit it is working perfectly. Could anyone guide on this.
    You need to have the empolyee role for BP ..goto BP and got here dropdown for ur bp and choose role Employee and then enter ur userid
    also make sure that u have the message processing role
    Hope it clarifies ur doubt and resolve ur prob
    Regards
    Prakhar

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