I had that happen with my PIV with all latest chips/firmware and with an A4000T too, but it was the other way around. The 4000T would see the card, my 4000D would not. I tried everything and pretty frustrating it is swaping cards all around. I wasn't even gonna bother but decided to get another daughterboard for the A4000D that was going cheap on eBay. It worked! Even regretted after buying it thinking it would make no difference but that was it. I'd say change the caps but it might not do any difference. Maybe it's just some electrical compatibility with some boards, the daughterboard that was failing was in pristine condition, looked all new and shinny, much better than the one that worked! It even worked flawlessly with an A4091 and a Cybervision64 at the same time, and we all know those are pretty demanding of the ZIII bus.
I did notice that they had different chips on them (daughterboards on A4000D have 2 chips), so maybe try identifying the equivalent chips on the A4000T (if they exist) and replace them, if changing caps doesn't work.
