I looked around and found many people with this issue, but most of the bug reports have been closed due to being inactive years ago ... some because scroll-lock fixed their issue.
The issue is that when the mouse is controlling the camera of the game (in my case, Minecraft), the camera spins along an accelerating spiral pattern that goes from viewing "straight up" to "straight down" and simply spinning.
I've tried checking "relative motion", and I've tried scroll-lock. While they appear to behave (I don't know how to test relative motion, but scroll-lock locks me to either monitor), it does not fix the problem.
Interestingly, the game appears to actually "work" until the character moves, meaning, the camera behaves until the character takes his first step.
I'm running Win 7 C2D (E6600) server box with an Ubuntu 10.04 P4 client box. It doesn't matter which box I run the game on, nor does it matter which side the client screen is on. I'm running the 1.4.2 windows beta version and the packaged version for Ubuntu.
... none of those actually appeared to /resolve/ the issue. Maybe the solution is buried in the noise? The only "solution" I have to play games with camera controls is to shut down synergy, which doesn't seem like much of a solution.
I'm also a Minecraft fan, and I've also had problems with the mouse in games. Some times you can enable relative mouse moves and lock the mouse to the screen, but it doesn't seem to work for me with Minecraft. A temporary work-around is to stop synergy while playing Minecraft. Please wait for a bug fix.