Hi Chris,
Sorry I couldn’t have helped sooner but I saw your post when trying to solve the exact same problem. I’ll post my solution now, for posterity.
In the Sequence Settings, under Video Processing, choose Always Render in RGB. It seems that rendering ProRes video in YUV can be problematic. I haven’t read up on this yet, though. Changing to RGB solved this issue for me.
Note that you must make this change on every effected sequence.
Best,
Jake