I'm not really sure which AE version you're running; I'll guess at CS6. Is it up to date, as in version 11.0.4?
I see you're NOT using multiprocessing, which is good.
And just as a workaround -- just to get the project out the door -- you could always render out the comp in a lossless codec, then just put the overlay on the imported, newly-rendered file in a new comp.
How big is the jpeg on the top layer? If the scale is close to 100% there should be very little effect on your composition.
Rick, the jpg is pretty much the same size as the stage area when I bring it in. Just increasing the width to 120%.
Dave, the version I am using is CS6 and it is 11.0.4. I was hoping to not have to use a workaround but that might be my only option. Thanks for your help!