I'm not sure my problem is exactly the same, but I will add it just in case it's related.
This problem occurred before the patch in December, after which it disappeared. It has resurfaced shortly after the patch last week. I notice it most from 10am-5pm EST, but it still happens occasionally during other times.
I will be moving along in a bot, with ping around a steady 150 (I believe this is about average for US), which is no hindrance to game play. However, every 5-15 seconds my ping will shoot up for a second or two and then drop down to normal.
This event causes my bot to stop moving, and when I attempt to restart autorun, I jump forward as though autorun were still engaged the whole time, only my screen wasn't updating my movement.
Multiple tracert to perpetuum show no problems, except for 260ms at the last few hops. No other programs or games are affected in this manner, leading me to believe it is not a problem on my end.
Here is a link to a fraps of the occurrence on youtube. Hopefully you can make out what is happening.
http://www.youtube.com/watch?v=TR8SV_qVCR4
You can see that all other objects and players continue to update, while the movement of my bot does not. The sudden jerk of my position is what happens when I press a movement key or autorun after it freezes.