There are a few popular PC BIOSes: AmiBIOS, Award, Phoenix, and others. They all work in a similar way. None of these BIOSes understand or know about partition tables. They affect partitioning indirectly.
The following occurs when your computer boots up:
Steps (3) to (5) involve programs communicating with the BIOS, to ask it to talk to the disks. There are two ways of talking to the BIOS to do this: by using CHS (Cylinders Heads and Sectors) or LBA (Linear Block Addressing). Older BIOSes will only support CHS. New BIOSes usually support both LBA and CHS, although CHS support may be phased out in the future. (CHS is generally considered to be a horrible legacy system.)
Steps (3) and (4), performed by the boot loader, will always use the same access method -- either always LBA or always CHS. In the case of the Windows boot loader, this is determined by the LBA flag on the Windows boot partition (see section 2.4.16 set for information about about flags). In the case of Linux, you will probably be using either LILO or GRUB as your boot loader. GRUB uses LBA if it is available, and CHS otherwise. LILO requires that you choose when you install it (with the linear, or lba32 options).
Step (5) - IO done by the operating system - only Windows does its IO through the BIOS. [We still don't know enough about the problems, but it seems Windows can have its own problems with CHS mode. People have told us about occassions where Windows corrupts its own file systems, etc. It's really hard for us to know what's going on. We strongly recommend you use LBA, if you can!]
So, there are 3 possible situations, which are all covered here:
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