Will document this more:
The problem was if you were using 32 bit png files (as in opposed to 24 bit ones) BlitzMax assumes the mask is already present in the alpha channel of the file and does not overwrite it by making transparent all pixels set to the maskcolor.
It does mean however that if you can get to grips with how to edit the alpha channel in your paint program you can leave the mask color stuff behind altogether.
The problem was if you were using 32 bit png files (as in opposed to 24 bit ones) BlitzMax assumes the mask is already present in the alpha channel of the file and does not overwrite it by making transparent all pixels set to the maskcolor.
It does mean however that if you can get to grips with how to edit the alpha channel in your paint program you can leave the mask color stuff behind altogether.