ipod software update question

in iPod + iTunes + AppleTV edited January 2014
I have spent the better part of the morning working through a problem with my 40GB iPod. I think I figured out what happened, which I will explain, and am looking for a little feedback about how to proceed.

I am 3 days into a switch from PC to 15" PB 1.25GHz. I updated to 10.3.3 as soon as I got the PB up and running. I got my iPod a few months ago and formatted it on my PC with disk mode enabled. Everything worked fine when I moved my music library to the PB with podworks. However, this morning I ran software updater and it showed that iPod 2.1 (for OS X) was available. I downloaded the update and attempted to install. That's where the fun began.

When running the updater the iPod would disappear and not remount. I think the problem stemmed from trying to update a windows formatted iPod with the latest version of the mac software. Everything works fine if I click "cancel" when iTunes asks me if I want to upgrade to 2.1.

What's the best thing to do: reformat the iPod and install OS X iPod 2.1? Leave the current windows version 2.0.1 installed? If I leave the windows version on the iPod is it possible to disable iTunes from prompting the OS X 2.1 update every time I stick the iPod in the cradle?

I guess it makes sense to reformat to iPod OS X 2.1 now that my home computer is a mac. However, I use my iPod at work on a XP box for both music (using eph pod to play through windows media player) and as a hard disk for file transport between office and home. If I reformat to mac version 2.1 will I still be able to use the iPod as a firewire disk on windows machines?

Thanks in advance!
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