HI All,
Thanks for the replies, but we managed to figure it out yesterday. We were making 25 of those files as a batch process. We decided to change it to process the files one at a time in the program and that artifact went away. We still don't really know why it was happening, but it isn't happening after we slowed down the processing by making them serial instead of batch style.
If the Adobe guys still want some sample files to investigate, I'd be happy to email them to you.