I suspect that you'll have to install the compatibility jumpers on your hard drives. They force SATA 300 drives into 150 mode. You should look into this on your drive manufacturers web site. Some drives come with the jumpers, others don't. They are very small jumpers and you might have to get them from your nearest computer store, I would not recommend that you try to use motherboard jumpers as they are too big. Hope this helps.
You just have to set in bios to use the SATA ports as primary ports. If you have both ATA and SATA drives, you should have a menu for this also. Most 300 ports are backward compatible, and will run both 150 and 300 drives. With or without the jumpers. The fact that the bios recognized the pair before should be proof. When you flashed the bios, all settings were reset. Just boot to the bios, then set the menu accordingly..i.e. boot order, boot drive, onboard stuff..