Don't think able to remove Safe Mode. Check jumpers for starters. Begin and boot up of single HDD, your system drive - should be C:\
Unclip the rest can add back on later. Sort out C:\ first.
Go cmos for setup when your computer posts, and check your IDE or SATA disks because you should be able to boot into Safe Mode. If you can't, then the intrusion could be nasty.
Anything from logs yet?