That sounds strange.
Well, first of all take a picture of your case and current mounted hdd. That would allow us to see what is the actual problem.
Its very possible that first hdd is 3.5" and second one is may be an 2.5"one. Take a picture of the second hdd as well and post it here too.
Also you should know that bottom of the case is very unacceptable choice for placing such sensitive electronic equipment as hdd! I hope that these errors are because of bad cable contact, but...
You can download this free program CrystalDiskInfo
to check parameters how good are they. Take screenshot from it and post it here.