We had tried giving explicit permissions to the folder but it didn't help. So, we decided to just make the GPO as a User GPO so it will run as the user logged in. That seems to be working fine.
The one problem we're having now is that we modified the .settings file to force the Log file to go into a folder on each person's C drive. However, when someone runs the program with the /s flag, the First time it doesn't put the log file where we told it to. Then if they run it again, the Second time it does put the log file where we specified. I don't know if it's reading in the settings and running the scan at the same time so the settings don't take effect the first run or if it's a bug or what.
We're going to try running it the first time in Download Only mode to see if that works, and then run it the second time in regular mode so we can capture what each machine is doing.