Hi Aaron.
I have a similar problem, but only with the Audio, not the video.
It happens when we send projects to a different studio, using the same version (5.4.1), or when we receive projects from them.
Some of the sounds connect fine, others get the “Media start and end” message that pulls them out of sync.
I’ve noticed we got those messages when we tried to link to files in a different frame rate (23.98 instead of 24 and vice versa), or even audio clips that were originally edited in a timeline with different frame rate.
But now all our timelines are the same (23.98), and we’re still getting that for some of the audio files.
If anyone makes progress on this question please let us know.
Thanks
Gilad