GENERAL WORKSPACE COLOURS
Due to the default track colouring methods in Cubase 6, the general workspace may be many different colours. (This actually applies to all applications but can be especially noticed in Cubase 6).
We are not talking about the track colours but the overall appearance of the application.
If MEAP is having trouble recognising certain areas of your audio application this can usually be rectified by resetting the colours to the defaults.
The other (better) option is to make your own graphics (see MEAP Shots).