Mine play in stereo from both speakers (I've tried most of them) and on my mp3 player.
Did you convert them from Flacc? May have been a problem there - itunes maybe?
I can only think that the problem was how you got them onto your ipod (don't have one so don't know). The files themselves are fine so you've either lost one channel somehow or something in your input was wrong. No reason why they shouldn't play through both as far as I know.
I think iTunes has a problem with playing Flacc files?
Do they only play out of one speaker on the PC as well?
That should tell you if it's the files or the transfer to the iPod that's the problem.
There is an issue with some ipod sockets getting damaged and losing a channel but that would affect ALL of your music.
If it is all, Google
"ipod playing one speaker only" and meet a lot of other people asking the same thing