Hi, This is quite an old post but I seem to be having exactly the same issue as you.
I have swapped all the sata cables, re-seated the power connections but the hard drive randomly disappear from my system. I usually have to shut down the pc, pull the drives out, push them back in and boot back up for them to be detected.
I believe it maybe the connection between the sata interface at the rear of the bay where the hard drive slots into.
I have a mixture of SSD's and standard 3.5 HDD's.
The release buttons work fine on the bays and they click into place when pushed in.
Are the hot swap interfaces a replacable part and can this be ordered?
Love the case but the problem is driving me mad!! :-(