Yes, you probably installed Windows to the 2nd drive (either primary slave, secondary master or slave, or SATA2). Windows then named the drive "C" because it had the windows installation on it, but put the boot loader on the first drive (which should have been "C").
I'd tell you how to fix it, but I don't feel like taking the time at the moment. I'm sure someone else has the time, as for me, I'm going to bed.
<font color=blue>Only a place as big as the internet could be home to a hero as big as Crashman!</font color=blue>
<font color=red>Only a place as big as the internet could be home to an ego as large as Crashman's!</font color=red>