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From the Synergy FAQ:

How do I stop my game from minimizing when I leave the screen? Many full screen applications, particularly games, automatically minimize when they’re no longer the active (foreground) application on Microsoft Windows. The synergy server normally becomes the foreground when you switch to another screen in order to more reliably capture all user input causing those full screen applications to minimize. To prevent synergy from stealing the foreground just click “Options…” and check “Don’t take foreground window on Windows servers.” If you turn this on then be aware that synergy may not function correctly when certain programs, particularly the command prompt, are the foreground when you switch to other screens. Simply make a different program the foreground before switching to work around that.