Another very likely possibility is that none of this has to do with receiver or sub settings, you're just experiencing the rooms nulls and peaks. To test that, re-take your measurements again twice: One in the same place and an identical set 3' to the side. If they're a fair amount different, it's the room / sub interaction.
That can only truly be solved by repositioning the sub, repositioning the seating, or adding room treatments.
That's the problem I have in my room, and none of those three solutions are practical. So.... I've learned to live with it and stop chasing the perfection. Now, I enjoy my system very much, rarely worry about measurements, and imagine that someday I'll be in a room that's far better acoustically!
