Ok from my limited knowledge I would offer the following...
You sure that all your songs are on the ipod? Not sure of the capacity but if you have more songs on itunes than capacity on your pod, they are not all going to fit.
The only other thing I could think of is that you are actually putting the songs you want on and not accidently only uploading from a certain playlist?
On this train of thought, that may be a way round it; put your top songs in a specific playlist then only upload those tunes.
Bit vague I know....