[wlug] Help with BIOS geometry

I have loaded a dual boot up system several times, but I recently had my motherboard and harddrive replaced and this time the installation program came up with "unable to align partition correctly, this probably m,eans that another partition tool generated an incorrect partition table because it didnt have the correct BIOS geometry. It is safe to ignor, but ignoring may cause (fixable) problems with some boot loaders" Bloody hell, I "ignored and ended up not being able to boot the computer at all. It did not recognise the c-drive I have since reloaded windows from scratch (my linux partition is on a separate hard drive - but I cannot access it). How can I fix this problem with my BIOS? THanks John