Brian, I haven't had the difficulties you mention. The points I can comment on include measuring when the room is fully furnished, not empty. 8 measurements are available and should be used for the best accuracy. Doing them at the same point doesn't accomplish anything, but they also shouldn't be separated widely. Two a foot or two to the left and right, three more a foot or two in front and two the same distance behind should work well.
You should also try the Audyssey, rather than the Audyssey Flat curve for a less prominent treble.
You mention that Dynamic Volume is off, which is suitable in most situations, but you should be sure that Dynamic EQ is on.
The manual equalizer works as described in the manual, as an alternative to Audyssey(not an adjustment to it), which Dr. Kyriakakis has termed "crude". It only allows adjustments at nine specific frequencies, rather than the hundreds of frequency and time adjustments Audyssey does. Selecting it means that Audyssey is off.
Enjoy the music, not the equipment.