do you have the latest update for cs5 (ae 10.0.1)? it fixed many render issues...
another possibility is that with multi-processing on, ae is using too many of your systems resources (name ram). make sure you have enough ram allocated to 'other apps' (which includes your os). i would try setting that to around 25-35% of your total ram.
you can find other setting tips here:
http://forums.adobe.com/thread/543440
Kevin Camp
Senior Designer
KCPQ, KMYQ & KRCW