My mega only works on 1.0.1 IDE
You need to add a 100nF (0.1µF) capacitor between DTR and RESET so it generates a pulse instead of a constant LOW all the time the port is open.

The older IDE uses an older version of avrdude. The newer version of avrdude with the newer IDE has extra code for manually manipulating DTR to get around some issues with new versions of the FTDI drivers.