To clarify, there are two ways of setting devices on an IDE port. One is to set one device to Master with jumpers and then connect it to the END (Black) connector (preferred). If there's a second device, it MUST then be set to Slave and (preferred) connected to the MIDDLE connector (Gray).
The other option is to set BOTH devices (or only one if that's it) to "CS" with jumpers. But then the one plugged into the END connector on the cable will be the Master.
OP did the CS method, but plugged it into the middle connector, and that made it the port's SLAVE. Then the BIOS fixed up the mistake (there was no port Master as there was supposed to be), then figured out that, since it was the only HDD around, it would be used as the Boot Drive and it all worked. Smart BIOS dealt with the small errors and made it work anyway.