Yeah that's what I meant.
I have to say, that before I applied this fix, MKVs would either play or not play (mostly not play) - I never saw any juddering.
Maybe try using UI1 temporarily, see if that's anything to do with it? Sorry, clutching at straws here. Is this a new mobo, or have you had it working before?
If it were me, I would be tempted to attach a hard disk, stick ubuntu on it, and see if you get smooth playback with that. Then you'll know whether it's the hardware.