I am fairly sure this is because they are under the default 52mb. However, I added all 3 of these lines to the Rebuilder.INI file in the program folder and it makes no difference:

VTS_MIN_SIZE=1
VTSM_MIN_SIZE=1
DISABLE_UNREFERENCED_REMOVAL=1

Do these functions not work on the free (.98) version? Is there something else I am missing that can have it just skip VTS files? I am on windows 8