No it doesn't happen unless there's Flash content. It seems to happen most when I have a browser windows open on both monitors. Especially when I make a flash video (live.twit.tv for example) full screen on one monitor.
That's very odd. I use two or three monitors all of the time and haven't seen this with my Macbook Pro. Could you please open a new bug report on this over at bugbase.adobe.com? Please post back with the URL so that others affected can add their comments and votes.