I'm seeing this in 2016.28 as well. Here's what I've done to create/reproduce this error...
When I set the black transparency value, the value seems to "stick" until I do a copy/paste into the layout. Then, the transparency value resets. I've seen it reset itself to a value of 1 and a value of 3. It may have reset to a value of 2 in between them, but I didn't notice it, if it did.
I'm trying to set the black transparency for a number of my models to 100, as I am layering them on top of one another in my layout and want to be able to "see through" each element when they're off. For example, I have mini trees that are each 3 colors of standard a/c lights. To make the effect, I'm layering 3 models on top of each other.