It depends on what's causing this. Recently we've seen an increase in infections by the TDSS rootkit.
At work we clean the partition table of it with Trend Micro's command line scanner - which renders the system unbootable.
Then we run Startup Repair 3 times from an installation disk.
If that doesn't allow the system to boot, then we go into a Command Prompt and run:
and
So far that has fixed every instance of this infection. Every system that I've tried it on has been SATA - so I don't have any knowledge about the Slave/Master differences.
BUT, be aware that I am
not an anti-malware professional - so backup your stuff
BEFORE trying any of this!