The reason for this is that mpt doesn't adhere to the vst(i) standard very strictly. According to the standard, all the plugs should be processing silence when they're not in use. However, mpt seems to put them into bypass, or pause them, or something like that, when you hit stop. So fixing it would mean that mpt would have to be continually processing audio/midi to and from the plugs.
In most (all?) other music software, you can hear that they implement the standard correctly. For example, when you hit "stop" in cubase or fl studio, your reverb tails will die off, volume envelopes will stop, and so on. Basically, stop should start sending silence from all sampled instruments to the plugs, and send the "all notes off" midi message to the plugs.
Workarounds:
1. Stick an empty pattern at the front of your track. (This is what I do). Then, when you're rendering, the "pop" of noise will have died down by the time the actual track starts.
2. When you're going to get a "pop", first go to the instruments tab, and hit a key for the popping plug. This'll flush the buffer (and you'll notice that mpt will carry on processing nothing by the timer in the bottom right-hand corner).
