Will not use secondary color as alpha

One of the things I have always loved about about PMNG is the way it handles alpha. It is always had a genius approach that the second color is always set to alpha but using the program I have found that is not the case. Here are the steps to repeat the problem.

1.draw anything with one color.

secondary color as alpha

2.draw anything with the second color but only the second color.

secondary color as alpha(1)

  1. Using the brush grab tool right click to grab the image to turn it into a brush

. It should ignore the second color and make it transparent

secondary color as alpha(3)

but it does not

secondary color as alpha(2)
Please fix this was such a useful option.