With the current GUI, changing colors is possible, but it's quite complex. It would require digging into the python source (which ships with Qube) modifying the source files so that the appropriate widgets have the correct colors, then either running the interpreted version or recompiling & running a custom compile.
Instructions for doing such can be found under "Qube!GUI Reference" at
http://pipelinefx.com/docsOur next-generation GUI (soon to be in beta) will allow more flexible color control.
-Brian