I recently bought a GMK keycap set and noticed that a few of the keys weren't bottoming out. Instead of a "clack", I was hearing a muted "thunk". At first I thought this was a manufacturing defect - maybe the hole for the switch stem wasn't quite deep enough, preventing the keycap from being pressed all the way onto it. Upon closer inspection, I saw that there was a piece of plastic left behind from the manufacturing process:

This extra plastic piece was catching on the switch mount, preventing the keycap from fully bottoming out. I just took an xacto knife and trimmed off the extra piece, and the keycap was fine after that.
I don't have anything else to add; just check underneath your keycaps if some of them aren't bottoming out. This is my second GMK set and the first one didn't have any keys with this issue. I've never bought any other brand of custom keycaps, so I don't know how common this issue is.