Actually, you're experiencing the opposite of a wolf tone, which is a dead spot. In a nutshell, what's happening is that the neck is resonating sympathetically at certain frequencies, absorbing the string's energy. It has to do with the stiffness and mass of the neck, and since you can't make the neck stiffer the only way to address the problem is to change the mass of the neck. You can either add weight to the headstock or reduce weight. The easiest thing to try is the Fat Finger, which is a brass weight that clamps to the headstock. Others have changed to heavier tuners and even gone as far as to embed lead weights into the back of the headstock.
Fender Fatfinger Bass Sustain Enhancer: Shop Accessories & Other Musical Instruments | Musician's Friend
EDIT: as a quick experiment to prove the point: in the playing position, take your bass and touch the headstock to the nearest wall (gently of course). Then play your A on the E string and hear how much more sustain there is.