Since quark version r1.5-128 and beyond I can't seem to get the clean glass, varied bricks etc to work. There was a note in the changelog of "Rewrote the vanilla texture override system to be data-driven. This won't make a difference for players yet, but soon enough it will!"

Is there something I have to do to re enable this feature?

It's just those two that were broken, it was a bad copy paste on my part.