If you are satisfied that adding and removing the third harddrive makes the error appear and disappear, and if the drive is idle, then you have a broken motherboard. Myself I would run more tests to confirm but once you are sure that's that.
There is a possibility to explain things with a broken PSU but then every computer problem can be.
The harddrive might be broken and things might work if you exchange it. But in the end then the mainboard is still to blame, because a broken harddrive on one port shouldn't affect other ports, much less USB ports.
Before you get a new board, flash to the newest BIOS.