I just upgraded my PC with new Mobo, CPU, RAM, and a SSD. The Mobo is an ASRock 970 Extreme 3 2.0 and the Processor is a AMD FX6350, using 4GB of DDR3-1333. The new SSD is a Crucial M4 120 GB.
I booted up the system just fine and installed Windows 7 on the SSD. everything was fine until I installed my 3 other traditional HDDs into the system. Now it won't boot and says the OS is missing. When I go into BIOS the M4 isn't listed as an option on the boot menu, however it is listed in the BIOS hardware monitor. Does the boot HHD have to be on a certain port? Currently SATA_1 is M4, SATA_2 DVD, SATA_3 250GB Seagate Barracuda drive, SATA_4 1TB WD caviar drive, and SATA_5 250GB Seagate Barracuda drive.
On top of boot priority most of the time you have a hard disk/drive priority as well(will list ALL drives HDD and SSD). That should allow you to set the SSD. With that change, the board should go back to booting the ssd for you.
In general it should not matter what port you use as long as you setup for it in the bios.