Must be something with the way xACT is interacting with the shntool app. I didn't change the mode on any of the other apps like flac, shorten, etc. because I have had no problem with them, but that might solve the problem if people are finding the program is giving them errors/issues/hanging.
So, to summarize:
1. Running xACT as administrator and in compatibility mode.
2. Running the shntool app enclosed within the program in compatibility mode.
Success!
Edit: I changed the thread title to reflect that this was solved, maybe someone else will find it useful as well.