Boots using external USB/Firewire drive, not with internal SSD or DVD

I think I have a bad SATA cable or controller. When I try booting from the internal SDD or DVD drives I get 3 beeps, pause, 3 beeps. Normally this would indicate a memory failure, however I've replaced the memory with no improvements.

The machine boots fine from a USB thumb drive and also from an external firewire drive.

Could this be an internal cable problem? It effects both the internal drives, I'm concerned it may be the SATA controller. Any way to test it? Does it make sense the cable may be the problem with two drives involved?