I'm having this problem whenever I switch from one screen to another while running a fullscreen program on my windows. The program either gets minimized completely, or the computer brings the taskbar upfront. This happens whether my windows behaves as a client or a server. This is really frustrating since I lose focus of the program I'm running.
How to replicate
Open a browser on a windows with synergy 2
press F11 or make the browser full screen