Well the thing is everyone's metabolism is different. I don't lose any weight on speed - or if I do, I put it back on again within the next couple of days when I can eat again. That kind of 'yo yo' effect can have a negative effect on your metabolism, meaning if you're prone to putting on weight those little 'starvation periods' could actually teach your body to hold fat more efficiently during the times you do eat.
Another scenario is this: just say you're a healthy person. You jog, go to the gym, eat salads. You keep your weight down by doing all that. Then all of a sudden you get into drugs. You quit the gym, start getting too tired to exercise anymore, drink more alcohol, laze around on your ass during comedowns, eat junk food instead of doing your healthy meals (I'm not saying all drug users do this, but some may). I can imagine even the amphetamine-effect of speed (and to a lesser extent MD) wouldn't be enough to counter the 'fat ass' effects of that change in lifestyle.
I'm not saying it's just the drugs, but I have given up regular exercise since starting to take drugs, I drink more and I don't eat as healthily and that's definitely had a negative effect on my weight. Taking meth on a weekend doesn't make up for losing my focus on a healthy lifestyle.