The current cables from my sub to pre are the same ones I've been using for years and were dead quiet on my Ref31.

This crackling noise in the subs only appears when the 990 is in PLIIx...

My cable path from one of the subs is....
RCA to 1/4" TRS to Behringer DEQ2496
XLR from Behringer DEQ2496 to RCA to 990.

I do have crossovers built into the SVS amps - I'll try turning them on. Should I set them to match the 80Hz crossover? That seems like I'd be double filtering the bass - or should I set the SVS amp crossover a bit higher - like 100-120Hz just to make sure I don't get the higher signal bleed through?