I had a similar render issue on a MBP recently. My project was just a series of simple scales and crops on a very large image sequence, and after about 30 frames or so of speedy rendering, it ground to a halt.
I disabled the layer cache and set AE to purge every 20 frames during make movie. There's a secret menu in the preferences where you can adjust these—though this should be a last resort. Hold down the shift key, and keep it down. Click After Effects > Preferences > General. Continue to hold the Shift key, and click on the list of preferences. You should see a "Secret" item where you can make these changes.
If your renders were working perfectly, you would see a big performance hit for mucking with these settings; however, since they are not, it may help. Don't forget to reset them for your next project.
Walter Soyka, Principal
Keen Live, Inc.
Presentation, Motion Graphics & Widescreen Design
RenderBreak: A Blog on Innovation in Production
