About once a week I have this issue with Synergy where it will capitalize all the characters and start automatically holding downing the Ctrl key on the client machine. I tried to changing the settings in the options, but I still had the problem. Oddly enough a co-worker had the same problem who found an "elegant solution" to this problem.

Just press Ctrl + Alt + Delete on the server machine and then close the Task Manager (or hit cancel if you're logged in). For some odd reason this seems to fix the problem every time.