I agree.The second bay is not the best place for the second drive. After going through a similar experiece like yours. I just stopped putting any drive at the bottom bay. I think there are two reasons: one, the bay does not allow the heat from the drive to dissipate enough and two, its too close to the heatsink/processor.
I was afraid the heat form the heatsink might damage the other drive on bay one/top, I even attached a hard drive cooler, placed in such a way it blows towards the heat sink.