It is a design issue, and from what I've heard a great many Mesa amps have the problem.
However, the severity of yours does not seem to be normal. Most accounts I've heard of are just a one time occurance when changing channels, not something that happens every time.
Personally I have absolutely no problems with it, don't need to cycle channels or anything like that, I just need to start it on channel 3. Even if I don't start it on channel 3 I'll only get a pop 50% of the time, and it will never happen more than once after turning the amp off standby.
A guy I know also has the problem, no matter what he does it pops on going to channel 3, but again it will only happen once after switching it off standby.
Neither my amp or his pop loud enough to make it a real issue, so if yours is doing it to the extent where you're considering something different, try a new one first and see if pops with the same severity that yours does.
There was a rumour it might have something to do with the diode or rectifier tracking, so it might be worth switching all your channels to one and then the other just to see if it makes a difference. Probably won't, but it couldn't hurt to try.