Our student who is running the FMS tomorrow discovered the same E-stop issue last night. I didn't have time to investigate further.
Nice creative solution to the problem!
Another option for people who are comfortable with SQL databases would be to go in and manually clear the flag. I don't have a computer with the FMS installed handy right now, but I might look into making a script for that tonight.
I opened a bug in the CollabNet site
here.