This might be a stretch, and hopefully this doesn't apply to you, but try booting a known working disk ensuring that the floppy write protect is enabled.. (window open)
My A3000 does the same thing yours does, but in addition, it ruins the disks in this process so that they will no longer boot on any Amiga. With the write-protect enabled on the floppy, it works as normal.
My issue is not due to the drive itself either. Any drive tested did the same thing when placed into the 3000. I've not found the source of the problem, nor the solution.
