I'm experiencing the same problem.
I had thought that shaders had worked with transparency before, so I went and checked in some older versions [i'm currently using 4.8]. I went and looked in 4.41 to see if transparency had anything to do with the version, and the transparency is working with shaders on that older version, but in 4.7 onwards, the shaders produce that black stuff. I just wanted to add some information that may hopefully bring some light on this issue, and what in the updates might be causing it. I changed no settings between my clients, they have the same settings enabled on all 3
Here's Toribash 4.41
Then, here's 4.7
And finally, 4.8
What's breaking the transparency?