I really don't see a problem with the differences in response for the differences in placement. Here are the 2 Ultra traces overlaid for scrutiny:
First, there are differences in mic-to-sub in the 2 placements.
Second, one is in a corner and the other is not and in immediate proximity to an open door.
Third, unless conditions are very closely monitored, there is no certainty that the levels were identical between the 2 measurements.
Finally, as I've said before, the FF Ultra has a problem when corner loaded of driver distance to the 3 reflective surfaces of the corner. There is bound to be an erratic response through the crossover and so, is best placed against a wall and not in a corner.
So, the differences of a few dB and a big difference in response at cross are normal phenomena in such a comparison, IMO.
As far as using the amp in 2 channel mode to power each cabinet separately, it would help if you posted the specifics of the signal chain. I imagine that you're using a Y cable to get the input signal to the 2 channels of the amp and that you're subs are wired to 4 ohms each. I also assume that the cabling is of same lengths from the 876 to the amp and the speaker wire from amp to subs.
Q: Doesn't the 876 have 2 sub outputs? Are you using 1 and not the other or using both, 1 for each channel.
I would suggest to wire your subs to have a switchable input terminal from 4 ohms to 8 ohms. I would personally prefer to run the system at 4 ohms bridged to avoid the gain matching problem.
Of course, checking the voltage from each channel is the proper way to make sure each sub gets the same input, but is a PITA, IMO.
Ricci, LTD; does the DCX allow for level adjustment of its outputs from a single input? If so, it's looking more like the way to go with this system.