I recently put a SSD in my desktop and had a similar issue, Not all the time but most of the time, I had a seagate 1 terabyte (old drive) and the ssd for windows and it seemed to randomly pick which drive it would boot from, I went into the bios and it only listed the seagate in the boot order section, so I had only my SSD (OCZ Vertex 4) plugged in and then in bios put it as first boot device and after a good boot shut down and reconnected the seagate and it's been booting fine ever since. No idea why it was doing it or why it some times booted from the SSD and other times tried booting from the seagate but it all works now, Mine just came up the the loading screen and told me a windows file was missing or some thing like that.
Dauntae
Dauntae