Sounds as though you've got the 'main air' resonance at the low A, and the 'main top' at the higher one. Those are pretty normal pitches for those resonances, although a bit higher than I usually see on my 000-12 frets. It's not too hard to make some measurements, and then you'll know for sure. With some data to go on you can make some decisions as to possible remedies.
To find the 'main air' resonance (close enough):
Lay the guitar down on your lap. Pinch the low E string between your left thumb and finger down near the nut, while plucking the string with your right hand. You should get a dull pitched 'thunk'. Move the pinch point up the string while plucking it as uniformly as possible, and listen for the loudest tone. That's the 'main air' resonant pitch.
To find the 'main top' pitch:
Your ear usually assigns the energy of a higher resonance to a lower one if the pitch is pretty close, one sort of tone 'masking', so to hear the 'top' pitch clearly you'll have to cut down on the lower 'air' pitch. You can do that by holding the guitar up with your thumb on the end of the fingerboard and your fingers between the strings on the upper transverse brace. you hand blocks the hole pretty much, but try to avoid touching the edges of the hole. Now tap on the bridge in the center with a finger tip. You should be able to pick out a pitch, which will probably be somewhere near the troublesome note.
As John says, sometimes getting the 'back' pitch down close to the 'top' pitch can help these sorts of problems. Try tapping in the center of the back while holding the guitar up with the hole blocked, and see if you can isolate a pitch there as well. Depending on the back bracing pattern there can be more than one; try to find the lowest pitched one, which is usually also the loudest (but maybe not).
Strange as it may seem, sometimes lowering the back pitch can drop the pitch of the 'main air' resonance. The strongest effect will happen when the two are exactly the same, but you don't want to do that! This will give generally give you a major wolf problem. A semitone separation is close enough to couple strongly, and far enough apart to avoid troubles (usually). Given my druthers, I'd make the back a semitone higher than the top: in some cases I've seen the 'top' pitch drop over time, and you don't want it parachuting in on the back's terrain. Shaving the center of the back brace that's nearest to the active (loudest) area of the 'main back' mode will usually have the biggest effect. To be sure, you can add some temporary mass (such as poster putty) to the back over the brace. This will drop the resonant pitch, and you can play the guitar to hear the result. If you don't like it, remove the putty and no harm done.
Getting the top and back working together in this way can also help with the high A problem. This gets to be a complicated problem in coupled oscillators, and you can look up the math(s) in Trevor's books. The bottom line is that all the parts of the guitar work together to make the sound, and changing one can often change most of the others. Sometimes it doesn't take much of a change to remedy a wolf problem.
Note:
Trevor responded while I was editing this post. I'm adding another edit to say that he may not agree with everything in this now, but I hope won't be too offended... 
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