It was once explained to me (by an Ovation rep, in fact) in a way that my bonehead guitar-player marbles could fathom. A guitar (or bass) neck is effectively a big wood-chime, like axylophone tone bar. There will be spots where it wants to resonate, and spots where it resonates, but the vibration transmisson throughout the guitar will either reinforce or cancel in an unpredictable manner.
However, response anomalies around the 12th fret have a higher likelihood of happening, simply because that spot is near the midpoint of the vibrating string. Vibrations that travel either direction from that point eventually get reflected back to that point, and, if they happen to arrive out of phase and similar in amplitude, some cancellation will occur. If they happen to arrive at the same time and in phase and similar amplitude, a wolf note (or extra-lively response, possibly with some wierd overtones) can occur.
Basses are more prone to this simply because of the dimensions and frequencies involved, and dead spots and wolf tones can happen just as easily around other neat mathematical divisions of the string length. This explains why basses are nearly always recorded with some degree of compression, to even the peaks and valleys out.
Having said all that, I've found no rhyme or reason or good predictor for the phenomenon. I've been around guitars for over 40 years, managed a pretty sizeable music store, am good buds with the biggest vintage guitar dealer in Ohio, etc., etc. But it's funny, now that I think of it, of all the neck thru's I've encountered (I currently own four, two guitars, two basses), I have yet to encounter the phenomenon. All have ebony boards so, who knows? That could be a factor. BUT, Ive never owned one that had the phenomenon to a sufficient degree to make me resort to any sort of measure to counteract it, or to a degree that prompted me to sell the guitar.
