Some time ago I tried all sorts of things to get rid of the skipped frames, including (as far as I can remember) stopping tracker. I also tried formatting the SDcard to ext2/3/4, and having as little running as possible.
No consistenly good results, though having many things running does make things worse.
As I read on an earlier thread about video recording, the frame-skipping seems to occur when the bitrate reaches 4000kb/s or so. The most data-intensive bit is when the image goes from light to dark an vice versa.

Maybe encoding as H263 would help, at the expense of larger filesizes, but I doubt that is even possible without new drivers.
(sorry for going on a bit, but it bugs me that the N900 can do so much, but not record smooth video)