Sounds like it could be a connection issue.
It "could" be (and the things would make me happy!
Today I saw toying with my other A1200 and I found the same problem (without any HW change)... in this Amiga I have a SD/FF clipped on the mobo chips and, better pushing one of these connector, the problem is solved...
I will look better on the same connector on the other Amiga... but now the mobo is in repairing...
Really hard days for my Amiga hobby!