I have this same issue, but mine can’t be related to the codec at all! I am usually working with DV50 when I first noticed this a year ago in CS3. Now I am on CS4 and I just had this problem on a project which has only a couple motion JPEG and plain text and very basic filters. in watch the reder queue, it gets stuck on “retrieving footage” for layer 4. Layer 4 is a text layer that’s turned off!
Also, while rendering, the whole system is locked up, i can’t even tab to safari or calculator. I would like to be able to do minor tasks while it’s rendering but i can live without. But then when the rendering ends, my system is still unusable until AE quits.
The render queue says only 60% of 3GB is used – my system has 4GB installed. I am on snow leopard also and have run all the updates for system and AE.
Any ideas?