Trying to visualize the topology:
The normal setup has gone noisy, but which used to work ok (?) is - DAC output to amp input with RCA, (power) amp output to main speakers, preamp output to powered sub for each of L + R channels.
Questions
What feeds the DAC, and is it fed with coax or optical?
Is the crackling noise there when you unplug either of the RCA cables to the either or both of the subs at the preamp out? (NB turn the subs off or they will buzz)
Is the DAC powered by a mains power pack or does it have direct mains connection?
For a test, what happens if you move each sub in turn and connect it to the amp with a short, known to be fine RCA lead, and power the sub on?
Are there any other devices connected to any of the amp's input, such as TT etc?
Do the subs have any other input connections beside RCAs ?
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See, I'm assuming the subs have no connection to ground other than through the amp via the RCA wires, and you can test this with a meter, by one probe on the the outer collar of an RCA input plug and then the other on each of the prongs of its mains plug in turn (unplugged, obviously). The point is to establish if a ground loop is even electrically possible through the subs. This can be repeated with other devices. I'm still leaning towards a cable issue or some other fault (TBD), rather than a loop, as if I get your setup correctly it's a completely standard one that normally works without ground loops occurring....