I hate those stupid partitions ... recently a friend fried their HDD in a Dell laptop, so we replaced the drive, and fortunately there was a backup so I could do a full restore. In the process I said, meh, we don't need that extra partition, we'll reclaim the space.
Result: "Windows cannot boot due to a disk configuration error..." which is Bill Gates' long-winded way of telling you that the boot.ini file expected to find Windows in the second
partition and now can't find it!!
Solution is to fix boot.ini either by hand or using one of the methods Microsoft tells you about (I used a BartPE boot CD).
Of course this doesn't matter if you're reinstalling from scratch, just something to keep in mind if/when restoring from backup. --
"Against stupidity, the very gods themselves contend in vain" -- Friedrich Schiller