Sorry, I made you misunderstand. The holes do match, but when I stick it in the hot swap bay, the SSD doesn't reach the sockets...
I tried the one closest to the psu using my HDD, and it didn't get recognized by Windows. Changed it to the one where it is now, and works just fine. They are plugged in the same chipset in my motherboard. I suspect the power supply has something to do with this, as when I was building the computer, I noticed the cables coming out were ridiculously bent by the PSU support bracket...