Apparently if you leave an iPod plugged into your (amd64 at least) computer during the installer's (20060505) partitioning phase it will format the iPod regardless of any setting you've selected earlier. I'd guess this happens for any other usb connected storage device.
I should also note that this nukes the ipod system until the user runs the ipod updater's restore. Even then any non-itunes files won't be there, amd music will have to sync back.
I don't suppose you can provide any more information about how/why it kills the ipod. My wife probably wouldn't be too happy if I nuked her ipod nano (even temporarily) to try to reproduce this. You were using a CVS snapshot from 20060505 for this? If you could provide the installer.log and installprofile.xml, it would help a lot. If your install completed, they should be at /var/log/installer.log and /root/installprofile.xml in your new install.
The install failed later due to help2man failing from an ancient perl in the stage 1 tarball or something. The install.log is in the URL for he bug
Unfortunately, I don't have enough information to track down or reproduce this bug. Reopen if/when you have more info.
