Well, this could be an important hint. I've been hunting that bug for quite a while, now...
Could you explain more about how synergy works? What kind of events do X applications see when you switch? (Use xev to check)
Synergy is a tool that allows me to control both of my computers at once, using a monitor on each, but 1 keyboard and 1 mouse, both of which reside on my Windows machine (which I play DF on).
I linked to it previously, but can steer you there again if you need it.. For example,
here. Also, I've noticed it even does this when I not switching over to the other monitor.. To switch between monitors, btw, all I have to do is mouse over to the righthand side of my screen.. which does have the similar effect of 'tabbing out' of my active MS Windows program. Tabbing out also makes my screen clear, by the by.
I'll post my config file in a 'spoilers' below, so you can emulate my settings to see if any information can be gleaned there. I do not know if it behaves this way without Synergy running, but I could attempt it if you'd like.
Err.. The Xev thing. I'll check it for you, but as this process isn't running under Linux, I'm not sure if it'll help. Is there any info I can grab from the Windows side that'd assist you?
Well, the forum doesn't like posts as long as that. I'll send you a private message, failing that, I'll ask for your email address in a PM. One way or another, we'll get the info to you.