I chased this question for weeks, learning several small things along the way. So I may be able to give you a few suggestions.
1) You are using a Radio Shack meter to calibrate the SPL level and measure the frequency response. This is said to have a ±2dB error, although I have seen a thread citing even larger variation among RS microphones. The Audyssey retail microphone is also said to have ±2dB error. So you could see normal differences up to 4dB without anything out of the ordinary happening. The only way to improve upon this is to buy a calibrated microphone, then you will have better control on the frequency response during the measurement process.
2) REW drives one or two channels depending on how you connect it to the AVR. If you are driving two front channels with a single monaural signal, you will see only +3dB of gain due to destructive interference between the speakers. But the two channels fed to a single sub will show +6dB of gain. So if you are driving two front channels you should expect to see the sub elevated by at least 3dB because of the measurement procedure. You can avoid this by taking separate, single channel, measurements of the sub with the left front, and then the sub with the right front.
3) You can also see variation if your REW microphone placement does not match the position of the tip of the Audyssey microphone, both in height and in the horizontal plane. Audyssey actually tries to set the levels based on its evaluation of all the measurement positions -- in some sense an average of the six or eight positions. So it could be looking at a different value than you are seeing using REW at only one position. You can try taking six (or eight) measures in exactly the same position as you used during Audyssey setup and average these, to somewhat replicate its evaluation procedure.
If you visually add +3dB to the curve in the region of the fronts, it appears as if the levels of the peaks in that range are close to the level in the sub range, and the remaining differences could be attributed to variation between the two microphones. But you will have a better feeling for this if you take the separate, single channel measures, and compare those. Best not to recalibrate or move the microphone between the measures; you would like to see the sub curves from the two overlay each other cleanly.
Good luck,
Bill