You seem to have researched this a bit, so if my redneck explanation is insulting, consider it intended for the other people.
A bullet will fly well in supersonic flight and in subsonic. Whitworth rifles, 40mm rounds, etc. are examples of pretty darn accurate subsonic rounds. It's the subsonic realm that destabilizes a bullet.
Two good terms to understand-
Transonic- when there is a variation of velocities around the bullet, some of the air is supersonic, some of it is subsonic. Think of the Supersonic 'wave' (that you see as trace) catching up to the bullet and flowing across it.
Wave Drag- Shock waves created by air moving at supersonic speed around or near a non-supersonic object. (someone help me out if you have a better definition)
How does this effect a bullet? During transonic flight, air moves fastest around the largest part of the bullet (venturi effect, maybe?), however, it slows down to below the speed of sound before it reaches the rear. Since the whole bullet is not moving at the speed of sound, the supersonic shock wave effects the rear of the bullet and induces wobble/tumbling.
Nutshell non-scientific explanation-
The sonic boom that you hear from a supersonic bullet (or jet) is all the sound (or energy from the bullet pushing the air apart) compressed until all the sound waves are stacked on top of each other. Since the bullet is moving faster than the speed of sound, they stack up (really they are just sound waves that are very close together). That 'stack' of compressed air and sound has a lot of energy, anyone who's had supersonic rounds fired right over their head (think the pit at a sniper range) knows this from the sound- that little bullet makes a lot of noise.
During transonic flight, which I believe covers less than about 200m of flight, all of that energy sweeps back across the round from rear to front (think the cool videos of fighters breaking the sound barrier, except in reverse). This is what causes a supersonic bullet to wobble in transonic and early subsonic flight, and eventually tumble. Luckily, it happens somewhat predictably and we can obtain data on the range and on good systems like ATrag, however it's nowhere near as consistent as supersonic flight.