I am running Synergy 1.3.1 client on a SUSE 11.1 machine and the server on a Win7 machine.
Every once in a while (~once every few minutes), the client-side mouse and keyboard will freeze for several seconds and then wake back up again. Sometimes the freeze is long enough that I end up just moving over and using the physical mouse/keyboard (which always work fine). I've reniced the synergyc process to maximum priority which seems to have helped quite a bit but hasn't eliminated the problem.
I've monitored the processor/network/resource loads and don't see anything suspicious when the freeze occurs.
My previous machine was a SUSE 10.2 machine running the exact same client and I never had any problems.