i'm using 12.0.129, a 60gb video ipod with 1.2 firmware. ejecting with MC12 has always had the same results for me, tho with 11.1 the behaviour was inconsistent between builds. however the behaviour was always one of two (that i remember), that is;
1) ipod is stopped completey, disappears from tree view, no charging
2) ipod ejects, still charging, but remains in the tree view. you appear to be able to perform functions on the ipod like syncing, browsing etc, but it is merely an illusion.
Besides, I don't see how an iPod can be not charging when attached to your computer. My understanding is that when it is attached you can only get the "do not disconnect" message or the charging battery icon, and that in both cases the battery is charging.
the OS can cut power to the device. stopping it using Safely Remove Hardware cuts power to it, so it won't charge anymore (maybe you could check if you get the same results doing this with your ipod?). ejecting within MC is doing this same thing for me, though i'm not exactly sure why it doesn't do it for you. do you have any drivers installed for the ipod? i don't have itunes or any ipod drivers on my system - maybe that makes a difference?
or possibly your hardware setup doesn't allow for cutting power to the USB ports.
