Sadly, that can't be helped.
I recorded the in-game cutscene at 1600x900 so it would be the same resolution as the movies in the high-quality movie patch, and it looks quite good.
Not in my movie, it didn't. Granted, something like the Kreia's Fall movie would be longer and more difficult to match up, but it can be done using VirtualDub and Audacity.
Well, for one thing, it doesn't "flow" very well. The resolution changes take forever and part of the music is cut off. Secondly, one of the biggest gripes about TSLRCM that I've heard from people on other forums is how the multiple resolution changes can make the game minimize or even crash. The shuttle to Telos cutscenes are particularly bad in this regard. It's happened to me enough that I thought that doing something to keep those resolution changes to a minimum was a good idea.
I'm not asking for this to be part of the mod, but it is likely the only solution to what I think is a glaring problem.