Thanks for such a quick response.
Are you using the 64 or 32 bit version of eclipse indigo?
Which version of the Arduino IDE are you using?
Are you using the serial monitor of the plugin?
I am using:
64bit Eclipse Indigo
And I am not using the serial monitor.
Linux Mint is a fork of Ubuntu with no Unity, it should work just the same as if it were run on Ubuntu.
In your boards.txt file do you have the following line?
If so and you are not using the serial monitor than the plugin ignores the com port completely.
I have been using the default boards.txt file from 1.0.1, so there is no Micro listed. I have been using the Leonardo configuration from the boards.txt file and it works fine in the IDE. The micro was not added to the boards.txt file until 1.0.2, so I could try giving 1.0.2 whirl if you want.
I have checked the Leonardo settings and upload.disable_flush is set to true and setting it to false has no effect.
I wonder if perhaps the timing between opening and closing the serial port and running ARVDude is different for the Leonardo than the Micro ?
I also wonder why you have to select
Goto Window> Preferences >Arduino>Arduino and check Disable RXTX
For every upload. This is a global setting. Setting it only set a global flag.
When Disable RXTX is selected, does the plugin not try and reset the arduino?
Can you post an image of eclipse when you see the "message box showing eclipse is running AVRDude"