Hello to anyone who has used handbrake to convert files for their ipod....

I have the newest version of handbrake and am trying to convert the avi files to mp4's which will play on my ipod classic. I have tried the standard ipod 5g button and I have also tried custom and used 320x240 size...
both will load onto my itunes, but neither will copy to my ipod classic. Can you be of any help? My itunes is on my mac, but my ipod classic is formatted windows (but always has worked just fine with my mac itunes).
am I missing something?
the handbrake help section is of no help whatsoever, so was hoping somebody had used this combo on this form..
thanks for the help.