After Effects CS3 Renders Play "choppy" in FCP sequences.

Has anybody else noticed that your after effects renders, when dropped onto an FCP sequence and then rendered out look choppy?

It's odd because they play fine in the FCP sequence, but when they're rendered out, they play choppy but the rest of the footage that didn't come from after effects play fine.

I've noticed this ever since FCP Studio 2 came out. do you think it's apple trying to get people to use motion?

The only work around that i've found is to right click (from your project window) on the file and export quicktime>using current settings, and then re-import the render out of FCP and then when it's rendered from a sequence it looks ok, but that's a lot of extra rendering.

Anybody know what this is all about?