I don't know of any special configuration I might have, except I use synergy to share my keyboard and mouse between this machine and my Windows workstation. I have the Linux box configured as the server, so the keyboard and mouse are connected directly to my Linux workstation, which is where this is happening.
I would add that, in some additional testing, the flickering is not 100% reproducible, though I would say it's close. One potential clue might be that if I cycle to another window or desktop (i.e. another Linux desktop, not the windows machine) and then go back to the diff window, usually the flickering has gone away.