You formatted your computer? Wouldn't it have worked to assign the proper boot disk in the BIOS? Furthermore, partitioning your hard disk in two parts (one for the OS and apps, the other for your data) would prevent any data loss when you reinstall Windows.
I've got the feeling there's some issue with your computer, not the X5?
On Windows XP or Vista (or even Windows 2000) you don't have to disconnect the player, you can just yank the cable out when all transfers are finished. It shouldn't do any harm - even if Windows pops up a window to complain about "improper disconnect". I never lost any data by doing that.