Some time ago on Atari Area forums we talk about it. In that time You have connected the second POKEY IRQ pin. Did you disconnect this PIN? It should not be connected. The IRQ pin of second POKEY must be not connected to anywhere.
We talked about it here: http://atariarea.krap.pl/forum/viewtopic.php?id=4233
with greetings
Sebastian Igielski (a.k.a. Seban/SLIGHT)
Yes, you're right. It's a problem with my stereo upgrade. I have totally forgotten we have discussed it years ago.
F.