I've been able to work around this problem, at great length, by fidding with the transitions into and out of the slides which have videos. The rules I'm using are:
1) Never use a magic transition into or out of a slide containing a video.
2) The video should always start automatically via the "Start Movie" build in.
2b) The "start movie on click" box should be unchecked.
This means that it can be useful to pad the video with dummy slides before and after it to achieve the transition and video start behavior you want.
I tried doing an automatic transition after the video finished (with a manual delay), but that may also be broken.