Forget the SPL meter. Does something about the auto-calibration sound bad to your EARS?
As previously mentioned. Most low-cost SPL meters are notoriously bad, especially on the low end. It sounds like the meters that come with most of the newer receivers are much better and do a better job setting the proper levels than anyone could do with a handheld SPL and any kind of test tones.
It also does not matter where the gain on your sub is set if it is producing the proper level of sound. My 12" 300 watt sub has always been set on the low end of gain to get the proper sound level. With the autocalibration, I would try to keep it within + or - 5. Actually, I would think 0 would be the optimal setting, but personally, as long as it is less than 5 either direction, I would leave it be.
If your system just sounds bad with the auto-calibration, then, and only then would I look to another method. Then I would use AVIA, through your DVD player (PS3) since that is how you watch movies. Personally, I have always calibrated at something closer to my listening level, instead of reference, unless that is how you watch movies. Unless your receiver has a good dynamic EQ program, or you have all identical speakers, your level calibration may not be level at your movie watching volume.
Of course, this is all just one man's opinion and YMMV, but unless you have some very high level, calibrated equipment, forget the readings if the automatic calibration sounds ok. With all of that said, I have had mixed results on a few auto-calibrations from one to the next, so it may take more than one run, or adjusting a sub location, adjusting speaker angles, making the environment absolutely as quiet as possible, etc to get the best result, but I would try that before going back to the SPL meter.
