Are both the drives on the same IDE cable? If so check that the jumpers are set to Master and Slave and that the C drive is on the end of the cable. I`d also be suspicious of the CMOS battery. Does the computer time and date correct when this happens which might indicate it`s time for a new one.
If none of the above apply I would check the C HDD for errors. If it`s not spinning up quickly enough then the BIOS will not recognise it and it will go on to the next drive in the boot order.