If memory serves, this sometimes happens with JPEGs. I believe the solution was to open them all up in Photoshop and just resave them. You can do this in a batch.
Hey Jim, would you recommend batch converting to TIF at a resonable dimension for future projects like this?
I do that but it's just because I'm used to the FCP6 time when JPEG files were a pain.
I'm not a fan of JPEG myself. I use PNG as my default format. It's lossless, smaller than other lossless formats, and can have an alpha channel.
I like PNG's for video as well - never had trouble with PNG