When I first towered my A1200 I had big problems with the floppy drive. Similar problems to yours. Turned out I had screwed it in too tightly! Some of the mechanism of Amiga floppy drives is exposed underneath the drive, so screwing it in too tightly might "brake" it against the tower. So try loosening the screws a bit and see if that fixes it. Better yet take the drive out of the tower (but leave the cables connected) and try it again. Also, double check the cables are all in the correct way round.
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moto