Oh what I actually wanted to say, are you sure your libquicktime actually supports mjpeg?
I am on Gentoo linux here, and my libquicktime is compiled as following :
"X aac alsa dv encode ffmpeg gtk jpeg mmx opengl png schroedinger vorbis x264 -doc -lame"
(which basically means I get everything inside beside the documentation (which is mirrored online mostly anyway) and the MP3 encoding support (but I hardly ever use audio in video material))
Unfortunately, I have no clue if Ubuntu has anything similar to this, maybe different versions you can pick from the repository?
--
buZz
http://puikheid.nl/