I have a similar problem running Teeworlds 0.6.1 on my 64-bit Linux Mint 12 system with an open source graphics driver and an ATI graphics card. It doesn't always happen immediately, but sometimes at an arbitrary point into a match, the cursor will stop moving for a split second at random. The irregularity makes it very hard to aim. This problem occurs only with Teeworlds. (For example, I can play OpenArena and Minecraft without this issue.)
I didn't use to have this problem on Linux Mint Debian Edition, so it's possible there's a version difference or something else is interacting badly. The game also now occasionally overheats my laptop as well, whereas it didn't when I was running it under LMDE.
My problem has nothing to do with ping – As far as I'm aware, my ping is normal.