That's correct. I've experienced the same issue with my daughter's iPod in the past. My computer wouldn't fully boot with the device plugged into the computer.
Youcan prevent that in the future by changing the order of the boot-up devices. It sound like you have the USB port the Pod is plug in as your first boot-up device. Re-order so it doesn't try to boot-up their first. A beeter order is to put you CD drive frst, then Sata 0 second. The reason to put the CD drive first is in case you Sata 0 drive ever does really become corrupted then you can recover your PC from a boot-up on a CD. After reordering , leaving the iPod plugged in won't matter.
Normally you reorder by going into setup, interupting Bios when you first start with a immediate depression of the setup function key, usually F2 sometimes F8
Peace and Good PCing,
Forest Man
EDIT : sorry I ddn't read down far enough in the thread, Matt34 already answered correctly mea culpa