My settings on the sub:
Trim set to flat
Crossover set to bypass
Volume set to about 8 o'clock position
Phase 0
Receiver settings:
All speakers set to small
Crossover set to 80hz
Sub level -2dB
My guess is you don't have your receiver set right. Can you describe how you have your receiver settings, for ex., speakers (small/large), crossover setting, dB level for the sub. The Auto Setup should do a pretty good job, I assume you placed the mic in the primary listening position about ear level.
There should be a User Preset option to reset the receiver back to the factory defaults, look at page 101 in the manual, however, I don't think this will reset the autosetup settings. Each time you rerun the autosetup should clear out the previous settings.
You need to describe the popping sound to us more, are you using sub coaxial to hook to the receiver?
Have you tried movies with lots of LFE, or are you trying music? Please provide more information.
Randy