I don't know where to start with this kind of problem :'(
The above graph is both subs active, phase 160 on the Right, 0 on the Left. No mains.
The Right sub Xover is set to 100, the L Sub is set to 80
No Audyssey, No BFD Filters.
Now:
The above graph is both subs set to Phase 0, no mains, direct input to Sub-In on the amplififer, no BFD, no Audyssey.