Yeah, that is kinda weird though reboots are a great way to uncover previously undetected issues in all sorts of electronics.
is it on a level surface? i recently found that my ls421de won't boot if I tip it on it's face (I was trying to observe the fan speeds). If you were doing something strange like that then the drive coming somewhat loose might also explain what you see.... but I'm guessing you wouldn't do that.
I assume you've also tried the other "known good" drives in that bay and confirmed that the issue persists no matter which drive.
I've got a pretty high-res photo of the ts1400d sata connectors and surrounding components posted if you'd like that to compare to see if a resistor might have broken off or something. (I can take one of the ls441de if you'd like)
https://static.miraheze.org/buffalonaswiki/8/8b/Ts1400d_board4.JPGActually, I suppose you could try re-seating that board. I think the odds of that connection being loose are pretty slim but it's something to try if you're comfortable with that kind of thing.
You could also try reinstalling the firmware and force-reinstalling the bootloader as part of that process. There is an almost zero chance that u-boot isn't initializing that bay like it should that could be resolved by reinstalling it. I guess.
I can think of a couple of other things you could look at if you install Debian on it first, basically by manually enabling/disabling the power to that bay and seeing how far it gets into discovering/initializing the drive.
If all else fails it could still be good for a 3-drive RAID5.