I know this post is kind of old but in case someone surfs in here looking for the answer to this problem, the procedure I use is this:
1. Disconnect from EMS
2. Click on the "Lock" icon that can be found on the FTC tab "Settings"' (this appears once off of EMS)
3. Right Click FTC in the System Tray and select shutdown
4. That's it
Before anyone says "That doesn't work" there is one more piece to the puzzle that must be satisfied before it will work is that the logged on user must be a member of the local admins group on the endpoint. I struggled and struggled with this until one day I tried it as the local admin account (not a domain account) and it worked so I then tried using a domain account that was a local admin and it shut right down with no complaints.
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