What is doing the disk check, your OS? Windows XP, Vista? Mac? Under XP you can hit esc to cancel the check but I don't think there's any way of stopping it completely. You obviously have some sort of issue so I would advise fixing the problem rather than masking it.
BTW, a single physical drives can have more than one logical drive, so C:\ and D:\ could actually be located on the same drive... there's nothing abnormal about that, unless you've never partitioned it that way.
