When running the arduino software under Win7 the theme will be changed to aero basic for compatibility reasons. This doesn't make much difference really, but I wanted it to keep the theme from changing.
I know that the arduino software is based off the processing.org software, the processing.org software doesn't change the theme.
I just deleted the java (Java2, Version 1.4.2) folder from the arduino software and replaced it with the java (Java, Version 6) folder from the processing.org software.
The ardunio software keeps the aero theme on and works just fine as far as I can tell, I have used it for a few hours now.