I'm working on a stop motion using legos right now.
Rocking at 15 FPS and after a whole weekend of problems I finally got the first second of footage done yesterday.
Yeah.
Anyway, for my fellow filmers out there who have a flicker problem with their lights (when the lighting seems to change a lot) there's a program called VirtualDUB. I don't know what it costs. I just got it of TPB because I don't like SourceForge (the site the primary download is hosted on).
After you've got it downloaded, get a plug-in called "MSU Deflicker".
Here's a tutorial on where to go from there.
http://timelapseblog.com/2010/01/09/hdr-time-lapse-deflicker/Unless you're really anal about effects, all this does is stop the annoying flicker.
I just finalize my animations through Monkeyjam to an avi file in the highest quality and toss it into the program, then add that filer.
It's fucking amazing.