I have a Repulse audio card that worked great for years on my A2000 with a PP&S 2000/040 card. Then when I updated the CPU to an 060 card suddenly I got crackly noise when recording.
I also tried this card in an A3000 and again got crackly noise only when recording (either via analogue or optical inputs).
Very strange problem I can only guess might be noise on the Zorro bus....but I really don't know.
Sorry, not very helpful, but it may offer some clue. Have you tried the card in another Amiga?