Jose,
PTE 9 uses same video encoder as PTE 8, it's only newer version. We use default parameters for the video encoder and we set only a few parameters. Anyway we can't do anything with a problem which you described. Sorry.
As I understand this situation, it's not guaranteed that any two MP4 video file (even encoded with same parameters) can be joined correctly.
I will check again with different parameters later.
Try to reproduce this problem with as possible short projects and then send me these 2 projects with all files in a ZIP archive.