Fishing, When you run your tests with the SPL meter, set up as Al suggested and using your test disc, be sure to chart your results on a graph. This will allow you to have visual evidence of the changes you experience and will serve as an easy reference if you try moving your listening chair or speakers which you should also note on your graph. This will serve you well on your current problem, but it will also serve as a base in the future should your start to move your stuff about. It's a bit tedious, but considering all of your efforts so far it's worth while to solve or rule out possible issues.
Also, room temps can affect sound levels at some frequencies somewhat so I would note the room temp when the tests are made so you can compare them to later tests at different temps.
Another thing you can do is to disconnect one speaker. Then set up your mic/SPL meter about 3ft from the center of the connected speaker. Then run your test and chart it. Then disconnect that speaker, connect the other speaker and run the same test. This will help you rule out problems with the cross over in either of the speakers because they won't measure the same. (I once had a new pair of speakers with a bass problem in one speaker created by the manufacturer's mis-wiring a cross over. One speaker was flat to 32hz, the other rolled off starting at 100hz.)
Hope that helps a bit.
