OSX Partition won't mount. Permissions seem wrong

OS X was spinning and spinning when trying to shutdown so I held down the the ⌽ Power button to force shutdown.

Current Situation:

1. I cannot boot to OS X directly, I first have to boot to single user mode and manually mount the OS X partition (/sbin/mount -uw /) then reboot and it works.
2. Folder permissions on the Windows side are all screwy, even as admin can't save file to desktop etc.
3. I remote to desktop (XP) via Citrix and when I try to copy folder to OS X from the Citrix XP desktop (OS X drive appears in Windows) it will create the folder then say it cannot write to it. A check in OS X shows the folder is created as read-only for everyone.

2(*) and 3 may be unrelated and require an alternate thread (happy to create such) but I have them here for completeness.

Possible Causes:

1. My computer was slow to sleep so I ran the following commands in Terminal based on an article about Mavericks issues and then I repaired permissions.

   sudo defaults write /System/Library/LaunchDaemons/com.apple.coreservices.appleevents ExitTimeOut -int 1
   
   sudo defaults write /System/Library/LaunchDaemons/com.apple.securityd ExitTimeOut -int 1
   
   sudo defaults write /System/Library/LaunchDaemons/com.apple.mDNSResponder ExitTimeOut -int 1
   
   sudo defaults write /System/Library/LaunchDaemons/com.apple.diskarbitrationd ExitTimeOut -int 1
   
   sudo defaults write /System/Library/LaunchAgents/com.apple.coreservices.appleid.authentication ExitTimeOut -int 1
   

2. Recent upgrade to Windows 8.1

What I have tried:

1. Disk Utility from OS X, recovery partition and TechTool edrive (10.9 compatible version). Results:

   Incorrect number of threads but cannot fix.

   Repairing permissions just has a problem with one printer.

2. Techtool Pro (refuses to do a volume rebuild)

3. fsck

*) Sometimes I can get the OS X to mount in these programs and sometimes not.

Is there a permissions or partition table issue or something else? Does anyone know how to reverse the command line settings back to their original values?

My setup:
MacBook Pro 2011 17" (GPU fail seems imminent)
Bootcamp with OS X 10.9 and Win 8.1
MacDrive (on Windows side)
Parallels 8

Solution 1:

Ok, I managed to fix but I did have to pay some money.

I ran Disk Warrior from my TechTool Pro drive and it was fixed. Below is the information that it returned.

• 1 file had a duplicate ID that was repaired.!
! • 17 files had a directory entry with an incorrect text encoding value that was repaired.! ! • 1 folder had a custom icon that was found to be damaged.!
! • 2 folders had a directory entry with an incorrect custom icon flag that was repaired.!
! • 3 folders had a directory entry with an incorrect text encoding value that was repaired.! ! • Incorrect values in the Volume Information were repaired.!
! • Critical values in the Volume Information were incorrect and were repaired.!