Write-protect sctors?

I had a probable rootkit in ubuntu dapper that proved to be more persistent than I thought possible.I did rkhunter and showed some anomalies in /dev/...Trying to track those dir's down proved elusive,even with root enabled(in ubuntu,root is disabled by default.You can still sudo, but no su without certain switches,)the dir's effectively hid from my view.
So I decided to reinstall a clean slate.This is when I encounter problems that don't make sense.
As the install progresses to the partitioning of the disc,I opt for the erase whole disc option.It progresses to a certain point and then quits with an error..repeatedly.
I filed a bug report with launchpad,but my question is this:Can any malware you are aware of write-protect certain segments of a HD,without BIOS support?Or is there a BIOS trojan that I'm not aware of in Linux?Is this even possible with a hardened system?
Is this even possible in any system,Windows included?
What I.m asking is : Can any malware write-protect sectors on a HD that survive repartioning?
Sounds really crazy,huh?
Thanks,Scott