I was running the SCALE verification sample problems using FULCRUM and the scalerte, both of which lead to multiple “files differ” messages, and many differences as the verification suite progressed. Not all files were different, but a majority were according to the output. The issue here was that all DIFF files for any sample problems that had the "files differ" message, were empty. Any sample problem that was identical returned the correct diff file ouput, "files are identical."
When I ran the same SCALE verification sample problems by navigating to C:\SCALE-6.3.1\bin and running “scalerte @samples/samples” or running it through FULCRUM, all files returned identical with no differences at all. There were then no issues with the verification when running from the bin folder.
I figure if there were problems with the pathing, FULCRUM nor “scalerte” would run, and even so, some of the FULCRUM differences are small, within 1 standard deviation, its not like it couldn’t find the sample inputs and nuclear data files.