This has certainly been one of the wierdest experiences I've ever had. So I tried plugging the drive alone in all the SATA ports and nothing happened until I got to SATA 0. As soon as I booted, the drive finally powered on (it never did before), but before I could get into BIOS to check if it's detected it started making a loud repeated banging noise (not the *click click* I know from dead drives), when I panicked and shut the system down. Still, I decided to boot again two more times, however, the drive did not power on any more.
After that, I put it back in the external rack and turned it on with no out of the ordinary sounds coming from the drive and then I tried booting the PC. Turns out, it refuses to boot if the rack's USB is plugged in. When I finally got into Windows, the drive seems fine with no bad sectors or lost data.
I'm still not sure why it doesn't work with the new motherboard, but after what happened last time, I'm not going to try again. I might fire Gigabyte a message and see if they have anything to say about it.