I've never used the PNP tools. On my 3COM 3C509 cards the little DOS
setup program let me turn PNP off, and I very happily did so. I took a
quick look on DejaNews for this card, and someone last March asked your
very question, and had two people reply to say they're using such a card
with absolutely no trouble.
At this point I'd say your best bet is to mail the NE2000 driver
developer and see if you can provide him with enough info to track down
the problem. It would appear to be beyond my realm of expertise. The
simple approach would be to get a different card.
Brian.