Merge 2 videos on iphone

Hi. I'm working at a project at which at some point I have to merge 2 or more videos and save them in a single file.
I would appreciate any ideas on how to do this (the formats are .mov, made with the camera) directly from the iphone. Would also like some references to libraries that might make the job easier.
What I've tried so far was converting them to .mpg (or some editable format), merging them and then converting the merged video back to a format supported by iphone. I've managed doing this using ffmpeg, but I'm having some problems at converting back, because the video is unwatchable (colored big pixels). I've tried this with more options (most found on web, which said that the command should work for making videos for iphone/ipod), but none of them worked for me.
(I've tried stuff like converting to mp4 and then back to mov and the result is the same, though the mp4 is watchable, so I'm sure that the conversion back to mov is the problem (or from mpg to mp4/mov)).
Thanks in advance,
Alex.

managed to do the merging using ffmpeg. I made a combination from:
http://www.dranger.com/ffmpeg/tutorial01.html
http://trac.assembla.com/legend/browser/segmenter/segmenter.c
and ffmpeg.c
I also had to play a little with AVPacket.pts and dts (from ffmpeg) so frames won't get skipped and video/audio remain synced. (I can't post the code)

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