This seems to only happen on very large after effects projects that contain 100's of comps.
AE checks the integrity of the project and saves temp versions of the project. Sounds perfectly normal to me. You may be able to get better results by regulalrly flushing the caches, so older versions aren't retained, but really, this sounds more like you need to adapt your workflow and splice out comps to separate projects on an "as needed" basis rather than keeping everything one large lump of data with all the consequences.
Thanks for the reply, but this wasn't an issue with earlier versions.
However, I do like your idea of breaking the after effects project into smaller groups... would also reduce the auto-save time.
Okay, I split my single large after effects project into 3 parts... each part has maybe 150-200 comps in it. This seemed to get rid of that delay. So thanks for the suggestion!