a4000 cr motherboard revision d faults

[Castellen]

Do check the 22µF capacitors C317 (by pin 1 of CIA U300) and the other 22µF directly behind the parallel port connector for signs of electrolyte leakage.  See the other threads on A.org on this same topic.
As one of the CIAs interface some of the floppy control logic to the system's data bus, it's possible the damage is here.

It's also possible one of the CIAs is faulty, particularly if someone has tried plugging something "wrong" into the ext floppy port.

If you have a digital storage scope handy, you can check the system is polling the DS (drive select) lines from 0 to 3 on power up.  That'd be a good starting point.

[Castellen]

Forgot to mention, you could just try swapping the CIAs over since it's less than a two minute job (assuming you can SMD solder) which will prove if the CIA in question is faulty or not.

Failing that, replace Paula, and if still no joy you can start looking for PCB track problems.

That would be the less diplomatic, but fastest way to track the fault :-)