well you need to realize that chemically there's no difference between the MDMA in different pills. the reason they have different effects is entirely subjective (mood, situation, time since your last dose, the contents and acidity of your stomach, amount of stored serotonin...); it's not something the test can detect. except of course for the amount in the pill which can vary widely.
the rate of a reaction is affected by concentration as well as by the 'order' (the number and ratio of molecules involved). so a small sample will react slower; if you only use a very small amount of reagent, the reaction will go *faster* since in all likelihood the testing reagent is in huge excess and the concentration of sample will be higher.
it's also very possible that the reagent may react with other things in the pill, possibly including impurities from the MDMA synthesis, which may include ketones and, in an extreme example, alkenes (sulfuric acid can add across double bonds yielding diols, which may affect the reaction)
however.. the biggest factor is definitely going to be the size of the pill. obviously a big one will be less concentrated and react slower than the same size scraping from a small one. this is a factor when you eat it too; small or crumbly pills will dissolve and absorb faster than big or hard ones. it's even possible that a poorly made tab (too hard) won't dissolve at all.
