There are 2 types of A/B boxes out there:

1) Passive A/B boxes; simple, inexpensive units using a footswitch to toggle between two outputs..some adding a second footswitch to combine the ouputs for the "Y" function. (both amps on) This can work fine when the AB box is placed AT THE END of a chain of various effects pedals, right before the amps.

 The first problem arises when (like me) you use a seperate effects setup for each amp, placing the A/B Box BEFORE all the effects. THIS is when you will experience horrendous POPPING sound while switching between amps. 

The Second problem (if you use Fuzzes or hi-gain pedals) being a very loud white-water sounding HISS should you ( for example; have a fuzz on side "A") then switch to side "B" without turning off said Fuzz.

The third problem is that you will get "loading" between the amps when running in "Y" mode where both amps are on at the same time, taking away highs and muddying up your sound. 

The fourth problem can be "phase issues" when running both amps in "Y" mode. When 2 amps are out-of-phase it can be very odd sounding, with an apparent loss in volume instead of the expected increase and a very strange EQ, like a wah-wah being on in a fixed position.

The fifth problem can be dangerous as well as noisy; when a "ground loop" happens while connecting two amps via an A/B pedal, the result can be a constant loud HUM and could result in a nasty shock, especially hazardous when stepping up to a vocal mcirophone!

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2) Active A/B boxes; some active boxes can alleviate the loud popping sound, but do nothing for the other problems common to Passive A/B/Y boxes. And they introduce a new problem; They convert your guitar's native Hi-Impedance signal to Lo-Impedance. And most great distortions and Fuzzes simply do not like to see Lo-Impedance signal! They lose volume, dynamics, become trebly sounding....it just changes everything for the worse.