What, exact, version number of AE are you using?
We'd like some screenshots, I'm sure. Especially of your render settings and output module.
Try rendering as a QuickTime with the Photo-JPEG codec.
Thanks for replying........I actually figured it out. I had moved the final comp in the time line in order to do a screen wipe with a black layer to reveal the footage....this messed up the layerst in the other masks.
I just exported the finished footage and reimported it and did the screen wipe in a new project. This fixed everything.
It's wonderful to have good people on forums who respond though....so again, thanks.
A screen wipe sounds like something you could do in Premiere Pro. It'd also be a lot easier to edit, add sound effects, and music in Premiere Pro. Just use AE for the visual effects, compositing, and any motion graphics.