May take sharing the scene to have a look at what is going on - for me, overlapping a decal across a plain cube and glass cube where the decal had a mask worked just as I would have expected (the glass became non-glass and took on the decal material where it overlapped and not cut out by the mask). The private uploader info is in my signature, or maybe a cut down version of the scene can be shared. Otherwise some screengrabbing of the various materials involved may be needed.
Also, just for completeness, I have to ask if the glass is in any way inset and perhaps the decal is not overlapping it as a result? And just for a known issue that is getting a fix, if you zoom in real close, it's not that the decal is being applied but tiled something like 20 times so there are in fact loads of small repeats of the decal in the overlap area?