Hi:
I have the complete set up like yours though not with the equalizer or the DNR unit but I am using a DBX 3BX , and the problems I was having was with the individual channels dropping out intermittently.
The fix , for me , was to take the Pre apart to access the RCA jacks on the rear panel and look at how these jacks are constructed. You will see the ground strap crimped to the barrel of the jack. I soldered the two parts together to fix my problem. These jacks are absolute CRAP ! I can change the jacks on the tuner and amps but not on the pre , the jacks are too close.
Check also the various connectors for the inter board connections , one or more may have come off or loose and check all the grounds for the boards to the chassis frame. The audio goes from board to board for some of the functions. A schematic may help to be able to follow the signal from board to board.
This sounds like a weird problem , if the above repairs do not help maybe a better description may help.
Do you have all the channels at the tape out jacks? What happens when you operate the mode , selector , tape monitor and adapter switches. Can you put audio into the tape in jacks and have all the channels?
Let us know how it goes.
Hope this helps
Ed