Sync iPod to Mac, but store files on Windows and Linux

I am an advanced user on both mac and widows system. I had my old 3rd Gen ipod where it was in FAT32 format and would sync to a Win machine. Then I could use the ipod to transfer data (ala external harddrive) on windows and mac platforms.
So now I have a 5th Gen Ipod and Itunes on my G5. Today I wanted to use the ipod to move some files between my work windows machine and home to my mac. To make a long story short the new ipod is formatted to be hfs+ journeled system, which windows can't read.
So I figure the easy solution is to reformat the ipod to be win-dos format, let it put the ipod software on, dump the library back and I should have a 5th gen with FAT32 that can be read by windows (or linux). So here's the rub
I used Disk Utility in OSX to partition the ipod several times. the first time I just specified ms-dos format (or whatever the disk utility calls a windows partition). All went well until the updater could not put the software on the new ipod claiming that it had to be in mac format. Then I tried to split the drive and parition into a large mac/hfs partition (for all the itunes files) and a small windows partition for the ipod (for data file storage). The problem is that the updater kept selecting the fat32 partition for installation (because I had to choose master boot record in order to be able to put the windows parition on there. at least this is what I suspect was happening). Two partitions woudl mount on the desktop, but only one would control the ipod.
So why not just let the windows parition be the one partition that had the ipod control software on it, you say? Because then I'm back to the problem that the iPod Updater won't deal with updating the windows partition.
Any ideas on a work around?

My concern is that when I have to update the iPod (in the future), will the windows based updater software be required?
Only if you want to continue to use it on Windows machines.
If you want to use the Mac Upddater, it will not be read by Windows.
If I do what you are suggesting, will the ipod return to being a resident mac based sycing device even though the first update/install of the ipod software was on a windows machine?
No. You can use it on both/either Mac and WIndows.
This is why I thougth some sort of partition with space set aside for the windows partition would be the workaround?
The iPod Updater formats the entire disk, not a partition.

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Sync iPod to Mac, but store files on Windows and Linux

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