Quote Originally Posted by jasonrudolph View Post
...Most of the problem comes from when...you need to decrease the intensity of the image on the output...and the top layer starts to become transparent and shows the layer behind it...
A Trick for this I have posted in another thread is to take your top layer and decrease the RGB simultaneously to darken the layer, the same way you would when you use colorFX 1 and 2 to decrease the brighness of each fx.

Conversely, you can also have another layer on top of the stack with Lib 000 and file 001 (which is black) and by fading that layer up, it darkens the mix.

Granted this isn't what you are talking about, but a fix for the issue.