I had the same problem with the LFE difference. I eventually lowered the LFE by about 4db based on the AVIA tones. This may be due to the RS meters calibration being off in the low frequency. If one tone is at a lower frequency than the other, the lower freq will read lower in volume on the meter, even though its the same SPL.

If you measure things using different inputs, you'll get different results, especially in the home environment. You just don't have enough control.