Sorry for the bump, but I have an update that might help someone else help me solve this problem. I have narrowed down the cause of the error "\Common was unexpected at this time." to be in the batch file _BUILD\munge.bat. Specifically, by adding pauses in the code (a pause before this line prompts to continue while a pause after this line won't go as the munge has already crashed). The munge crashes at the highlighted line
which is about two thirds of the way down the file. The only references to "MUNGE_BIN_DIR" are in this excerpt here.
Just to get through what it's not: I've installed the tools multiple times and the same thing happens, the directory it's installed in is above, and I've compared the files and folder structure to that on another computer that can munge and it's identical.
EDIT:
So I'd still like to figure out what was wrong with the original files, but after working on it for another 10 or 15 minutes, I found a work around. I assumed that since my munge bin directory would always be ToolsFL\Bin, I went ahead and deleted the highlighted line above (and the closing parenthese) to make the file always set the bin directory to this. The munge went on a few lines until it reached the munge common portion, in which case it failed upon running the _BUILD\Common\munge.bat. I looked in this file and I noticed the last five lines quoted above also appeared. After making the same changes, I could run a full munge properly with common checked.
I looked into the other munge.bat files littered about and noticed they had similar lines as well, so all my munges should work. I still don't understand, however, what was wrong in the first place and why the munge on this computer failed when it didn't on my other. Could it be an update to Windows NT that slightly changes how batch files are read?
If anyone can shine some light on this mystery, I would be very appreciative.