Okay, if it says its missing, try going here:
Right click My Computer, and go to Properties.
From here go to the Advanced tab,
Under Start Up & Recovery, click on Settings.
Then click on EDIT.
This should allow you to edit the boot.ini. If its missing it'll tell you its missing. If thats the case, you should be able to create one...
The reason its probably still booting up is because the BIOS knows what your main drive is anyway, but the boot.ini can specify which other drives to load up too.
It should be in C:\Windows I believe, but I can't seem to find it on mine...even though I definietly have one as I can access it and edit it
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Micro soft Windows XP Professional" /fastdetect
That should load your system up, if that was in place, and you only had 1 partition which was Windows.