The original 6280 puts out a pop if you turn off a channel off and turn it back on (one pop for each). Doing this rapidly, for changing waveforms at a fast pace, makes the sound a bit "dirty" (clickity). The 6280A (found in SGX and some CoreGrafx models) doesn't have this problem. Most emulators don't emulate this, but mednafen does (and even allows you to pick which version to use 6280 or 6280a).
Also, when you change waveforms, the new waveform pointer isn't going to align up with the old one, so there's going to be some clicking going on right there (square waves best hide this). It might be a thing on deflemask where he is doing something to soften this. This would be something that all emulators would emulate though, since it's a misaligned pointer in relation to the new waveform. So if it plays fine on other emulators, then it's a channel on/off thing.
