The iPods, other than the Nano 2G, do not charge properly from USB at present; there is no option in the menus for this, the manual is wrong (only the iRiver h300 and the iPod Nano 2G have this option).
They do charge when connected, but only at a very slow rate which is not sufficient to keep the battery topped up while the disk is being accessed. You will have to use the OF's disk mode if this is a problem, until this is fixed.