New Post: MCEBuddy video files won't import to iPod Nano via iTunes

Here you go, this is an exact replica of the settings you posted. This has been tested and should work with 2.3.14 and later:
Put this in profiles.conf and you should see iPod show up in your list of profiles.

[iPod]
Description=iPod compatible (H.264 MP4 width 480 pixel video and AAC stereo audio).
order=handbrake
handbrake-general=--deinterlace --verbose=2 -f mp4 -X 480
handbrake-video==-e x264 -q 20.0 -m -x cabac=0:ref=2:me=umh:bframes=0:weightp=0:subme=6:8x8dct=0:trellis=0
handbrake-audio=-E faac -B 128 -6 dpl2 -R Auto -D 0.0
handbrake-audioac3=-E faac -B 128 -6 dpl2 -R Auto -D 0.0
handbrake-ext=.mp4
handbrake-audiodelay=skip
FixedResolution=true
PreConversionCommercialRemover=true
AutoDeinterlace=false