There is a different variant file for micro and leonardo so I would not use leonardo to program a micro.
So try with arduino IDE 1.0.2 and enabled RXTX
When Disable RXTX is selected, does the plugin not try and reset the arduino?
Not at all. How do you go from "disabling RXTX" to "resetting"?
When you disable RXTX the plugin stops doing all com port actions. So no reset before upload (you have to press the reset button yourself) and no serial monitor. How can the plugin still upload? Because the plugin starts avrdude who does the com port actions.
Best regards
Jantje
PS If you fiddle around like you are; it is nice to warn the reader in advance.