I can also confirm that excluding the program location will not prevent MSSE from quarantining the files if real-time scanning is on.

The trojan must be permitted for every running instance of MSSE on the network, otherwise they will all take turns finding and quarantining the files.

This is likely a false-positive, but if the users run into the real version I don't think SE would worry about that either, so I am suggesting SE be replaced to anyone who calls our office with this issue.