Okay so as the title says my computer will not boot off of the hard drive that has windows installed on it. It tries to boot off my secondary one and just shows a black screen with a blinking line. Anyway, I went into BIOS and made it so my boot drive was the right one, saved, exited, then it boots off the right one. But once I turn it off, it does it again, tries to boot off the secondary. Also I was playing League of Legends, and my computer blue screen and crashed, not sure why it did this, maybe its related to my hard drive not being detected when computer starts up. I ran League again and checked volts and temperatures, all seems fine.
I would try to unplug everything except the boot drive. I had a similar issue when i had put in a drive from another PC. The result was my boot partition C was changed to E. I unplugged every hard drive except for the primary. The system booted right up. Your issue might not be the same problem but try it out and see what happens.