Can you set VO to use a 61 hz refresh?
The problem fixes when you restart the computer, yes? How about if you just close the X server and restart it?
There are some key combos that will cycle through the available resolution/refresh settings, but I forget what they are. Have you tried those?
Have you tried disabling the 50 hz option in xorg.conf?

Where did the original post go?

Fluffy, I have the same problem... What did you change to resolve this?

The key combos to cycle through your available resolution/refresh rates are alt-ctrl-keypad+ and keypad-.

But yeah, if your xorg.conf says your monitor can use refresh rates that it can't actually use, then the game will probably throw it out of sync.

Thanks a1k0n.

I'll do some research to find out how to edit xorg.conf to only permit the refresh rates my screen can properly display.