Help with converting Videos - Using ffmpegX

Got my iPod last week and decided to convert my videos today. Got a DVD on using handbrake and then loaded ffmpegx to load my other vids on. Once they were all converted to .mp4 I added them to iTunes - fine. Connected my iPod and bummer no deal. The DVD worked fine though.

I encoded the video at:
mencoder h264, 320x240, 400 kbps, 29.97 fps, no crop

Audio:
aac, 44100 Hz, 96 kbps

I followed the tutorial here: http://arstechnica.com/guides/tweaks/ipod-video.ars/3 but it's still not working. Anyone got any clues?