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