I've got the ponytail (no flip-flops - too wet and cold here)

Let's have a look at a couple of spectra (spectrums in the vernacular).
(BTW, if you click on these images it should expand the pictures to remove the scroll bars)
First lets look at "34-art-usb-sample2-stairway".
This one sounds gorgeous, no over-emphasis here, just a nicely balanced sound - this can be our bench-mark.

- 34-art-usb-sample2-stairway.png (34.06 KiB) Viewed 1943 times
Now that's interesting - see the spike on the extreme left (if I cursor over it I'm told 82Hz). That's the bit that gets hacked by the low frequency roll-off.
Then there's a bunch of three spikes (98 110 124 Hz according to Audacity). I'm betting that we will see one or more of these at a much higher level in some other recordings.
Here's "31-art-usb-dual-pre-sample1". Not to say this is a "bad" recording - it's still very nice, but every now and then I hear a "whoomph" - where's that coming from? Let's look at the spectrum.

- 31-art-usb-dual-pre-sample1.png (35.9 KiB) Viewed 1943 times
See the spike at 110Hz (got the cursor in the right place on this one

) Much more pronounced than in the first picture.
If you listen to the recording (listening is after-all the important part), then at first listening it probably sounds fine - nice and warm with plenty of detail.
But listen again - that note at 15.5 seconds - "whoomp" - what is that? Bottom "A"?
I tune to "A 440", so that would put a bottom A on the guitar at 110Hz.
The good news - your guitar is in tune.
The bad news - whenever you hit an open A string the fundamental of the note will be over-emphasised (with the exact set-up that you used in this particular recording).
What did you do different between recordings "34-art-usb-sample2-stairway" and "31-art-usb-dual-pre-sample1"?
I'm not sure - you probably put it in the notes a few pages back in this thread, but I've got the bath running so I can't look now. Probably just catching a bit more from the sound hole in the second one.
Guitars are supposed to resonate at around 100Hz (and at around 80Hz) - it gives depth and warmth to the tone, but when recording it is very easy to pick up too much from one part of the guitar and get a recording that is out of balance. (The 80Hz resonance is typically the one that feeds back first with live PA and is just above the bass roll-off frequency on a lot of mixing desks - fortunately it's pretty easy to tame).