I noticed that when I would get a UAC permission prompt on my Windows synergy client, I was disconnected from the desktop for about 5 seconds. During that time I was unable to use my mouse or keyboard on that desktop until the client reconnected.
I found an issue here: http://synergy-project.org/spit/issues/details/3311/ which is the same issue, reported back in July 2012! There is a simple patch, so I applied it (after struggling to get a working compilation environment on all hackers' favorite OS, of course), tested, and it works!
I am maintaining an unofficial synergy mirror on github: https://github.com/cha0s/synergy-unofficial oh, and the specific fix outlined here is on its own feature branch: https://github.com/cha0s/synergy-unofficial/tree/fix-3311-uac-disconnect. Now, to fix the fact that copying in Windows won't paste into my Linux... :)
I also built an x86 (sorry, x64 was beyond my tolerance for MSBS) installer with the fix included, you can download that here: http://www.cha0s.io/sites/default/files/synergy-1.4.19-Windows-x86.msi and obviously, if you don't trust me you can use the github branch above. No hard feelings.