There is a reason for that. The Check Levels routine in the Measurement screen and the Check Levels routine in the Settings screen use different values to generate the pink noise test signal.For some reason I can calibrate everything just fine at 75db, but when it's time to measure I have to increase volume to avoid a "level is too low" warning.
The Check Levels routine in the the Settings screen uses the fact that you have the Check/Set levels with Subwoofer pull-down selected to generate its test noise (this a band limited signal with a low and high cut of 30Hz - 80Hz).
REW wants to double check and verify that the end frequency of the sweep that you have selected in the Measurement panel roughly matches the test signal setting for sanity, and so its Check Level routine uses the end frequency as the test pink noise hi-limit cutoff. So, if you had (for example) 20KHz as the end frequency to measure for your sweep, and you were measuring your subwoofer, you can see how the pink noise would be different (between the two Check Levels) and as such the low level signal you're experiencing.
To measure a subwoofer you should have the limits of the sweep in the Measurement routine set to 0-200Hz.
Often, even if you have the levels and sweep frequency set correctly, a peak or dip in the response of the speaker being tested will have energy at a frequency that trips the sanity check and announces that levels are too low or high.
Simply return to the Settings screen and adjust the input level of the soundcard a bit lower and then run Calibrate SPL and carry on.
Your response looks quite good and I don't see much there that a BFD would correct. Your only trouble is between 30-40Hz and since you can't move an IB around, you're basically stuck with the problem, other than moving your seating position (and that may not help). This is (as I'm sure your aware) the biggest problem with IB's.how response looks and whether I should be EQing further (I do have a BFD in the chain, but no filters are set up).
Anyway, the dip at 40 is sharp and wouldn't be too audible. The one at 32 is a bit worse.
BTW, smoothing is not usually used on sub plots.