I've looked through the bug list and haven't found any earlier report on this issue, but I will have overlooked of course. It is such an obvious problem that I simply can't believe nobody ever reported it before. Searching through bugs is quite a job in here.

Description to replicate problem:

When having added a second layer, fill it with a different color then the first layer. Set the coverage (in Dutch -my language : Dekking) to any number below 100% so that you can see the layer underneath it. Then transform the layer (rotate, scale, shear, ...).

Now this happes : The transparency is completely lost, gone. That way, you can't effectively transform the layer to the layer beneath it, which could be a reference image, or an image in which you'd want to add an object (e.g. a vase on a table), where the second layer would contain that object.

Pretty basic and necessary thing to keep transparency settings in effect while transforming the layer. 

I hope it'll be marked as duplicate.

grtz,
Bart