I was having the same problem on mine (my google search brought me here) and after reading the posts I switched to the charger that came with it and my sensitivity problems went away. My first experience with my MT4G was with the old charger so I am very thankful to discover that the only thing I disliked about the phone was simply a problem with the charger.
As to how, if I had to guess I would say that its all about optimization. The stock charger provides power at a certain rate or level which is calibrated and optimized for the MT4G. The store bought one probably provides power at a generic rate which either provides too much power or too little to the phone.
Someone can correct me if Im wrong, I'm not an expert, but I believe when the phone is plugged in it is run off of the power from the outlet and not the battery. So if the phone is using the store bought charger its either not recieving enough power or too much. It's also possible that there is come optimized configuration on the charger so that the right amount of power is used to run the phone and charge the battery. The store bought one may just not fit that bill correctly.
Sorry for the long winded answer, just my thoughts on it. I appreciate the help from Tamosaur, really helped me out.