I don't mean this to be funny. But given that this is running the actual drivers. Would it be possible to take a standard PC floppy drive, and have it read at Amiga OS disc?
As an SRE/devops/platform engineer or whatever the title of the day is people want to give. I would have zeroed in on the difference between the working system. And the non-working system. Either adding and then removing, or removing and then adding back the differences one at a time. Until something worked. What I see is two things. 1) you have an environment where it does work. 2) the failing environment was working, then started failing.
Is my method superior to yours, no. It just is being stated to highlight the difference in the way we look at a problem. Both of a zero in on what we know. I know systems, you know code.