Windows – Cannot resolve %windir% / Cannot modify %path% or %path% being reset on boot

See Updates 3 and 4 below for how the issue has evolved

My computer (Windows 7 x64, Lenovo Thinkpad T530) is having an issue resolving %windir%. After boot-up, everything works fine. At some point a while later, the computer is suddenly unable to resolve %windir%.

Checking the environment variables window shows that it is defined.

Checking the registry also shows that it is defined as well. I've actually deleted the key and re-entered it to no avail.

After a reboot, everything works fine for a while. Does anyone have any thoughts on anything else I can check?

Update 1:
After thinking about it some, I have uninstalled the Konica Minolta Pagebox driver/program that was installed about the time this problem started happening (see comments below). The problem seems to take about 4-24 hours (I've never timed it) to manifest, so I'll update again after that.

Update 2:
Issue is still occurring. I came back from lunch and %windir% cannot be found. I did a test after a reboot this morning and put the computer to sleep, then woke it up. %windir% was still defined after waking up.

Update 3:
Per Daniel in the comments, I ran set before and after error and compared the outputs. The first thing I noticed is that on a fresh boot my %path% is 2000+ characters long. I pruned it down to ~375 characters and verified it in a new cmd window. I rebooted, checked the path again, and it was back to over 2000+ characters (it matched what I originally saw). I truncated it again and rebooted once more and the same thing happened. I deleted the path variable and created a new one; same thing happened. At this point all I can conclude is either I cannot permanently change my path OR the path is being reset by some process on boot. Any thoughts?

Update 4:
I edited my path via the registry method suggested below. I checked my path today after running for a while and it has grown from what I entered into the registry; it now has a few new entries and a lot of duplicates. The only new entries are from SQL Server 2012. I went to change this in the registry and I noticed that the registry does NOT match the output of echo %path%. Checking the Environment Variables from the Advanced Properties Tab shows a third version of my path.

Registry Path:
C:\Program Files (x86)\Microchip\mplabc30\v3.30\bin;
C:\RUBY193\BIN;
C:\Windows\SYSTEM32;
C:\Windows;
C:\Windows\SYSTEM32\WBEM;
C:\PROGRAM FILES\COMMON FILES\LENOVO;
C:\SWTOOLS\READYAPPS;
C:\PROGRAM FILES (X86)\COMMON FILES\LENOVO;
C:\PROGRAM FILES (X86)\MICROCHIP\MPLAB C32 SUITE\BIN;
C:\HTSOFT\PIC18\BIN;
C:\PROGRAM FILES\TORTOISESVN\BIN;
C:\Windows\System32\WindowsPowerShell\v1.0\;
C:\Program Files (x86)\Microsoft SQL Server\110\Tools\Binn\ManagementStudio\;
C:\Program Files (x86)\Microsoft SQL Server\110\Tools\Binn\;
C:\Program Files\Microsoft SQL Server\110\Tools\Binn\;
C:\Program Files (x86)\Microsoft SQL Server\110\DTS\Binn\;

Command Line path:
C:\Program Files (x86)\Microchip\mplabc30\v3.30\bin;
C:\RUBY193\BIN;
C:\Windows\SYSTEM32;
C:\Windows;
C:\Windows\SYSTEM32\WBEM;
C:\PROGRAM FILES\COMMON FILES\LENOVO;
C:\SWTOOLS\READYAPPS;
C:\PROGRAM FILES (X86)\COMMON FILES\LENOVO;
C:\PROGRAM FILES (X86)\MICROCHIP\MPLAB C32 SUITE\BIN;
C:\HTSOFT\PIC18\BIN;
C:\PROGRAM FILES\TORTOISESVN\BIN;
C:\Windows\System32\WindowsPowerShell\v1.0\;
C:\Program Files (x86)\Microsoft SQL Server\110\Tools\Binn\ManagementStudio\;
C:\Program Files (x86)\Microsoft SQL Server\110\Tools\Binn\;
C:\Program Files\Microsoft SQL Server\110\Tools\Binn\;
C:\Program Files (x86)\Microsoft SQL Server\110\DTS\Binn\;
C:\Program Files(x86)\Microchip\mplabc30\v3.30\bin;
C:\RUBY193\BIN;
C:\Windows\SYSTEM32;
C:\Windows;
C:\Windows\SYSTEM32\WBEM;
C:\PROGRAM FILES\COMMON FILES\LENOVO;
C:\SWTOOLS\READYAPPS;
C:\PROGRAM FILES (X86)\COMMON FILES\LENOVO;
C:\PROGRAM FILES (X86)\MICROCHIP\MPLAB C32 SUITE\BIN;
C:\HTSOFT\PIC18\BIN;
C:\PROGRAM FILES\TORTOISESVN\BIN;
C:\Windows\System32\WindowsPowerShell\v1.0\;

Environment Variables path:
C:\Program Files (x86)\Microchip\mplabc30\v3.30\bin;
C:\RUBY193\BIN;
C:\Windows\SYSTEM32;
C:\Windows;
C:\Windows\SYSTEM32\WBEM;
C:\PROGRAM FILES\COMMON FILES\LENOVO;
C:\SWTOOLS\READYAPPS;
C:\PROGRAM FILES (X86)\COMMON FILES\LENOVO;
C:\PROGRAM FILES (X86)\MICROCHIP\MPLAB C32 SUITE\BIN;
C:\HTSOFT\PIC18\BIN;
C:\PROGRAM FILES\TORTOISESVN\BIN;
C:\Windows\System32\WindowsPowerShell\v1.0\;

It looks as though the command line path = registry path + environment variables path. I attempted to set the registry path and the environment variables path to the same thing and reboot. After reboot, my path is now doubled, basically two back-to-back copies of the registry path above.

Once again, any thoughts?

Update 5: After talking with the IT Manager, he says he is fighting a similar issue on another computer. Both computers have SSDs (seems to be the only common factor). This may or may not be pertinent.