Ah I just remembered two things:
I once had a user with a broken trackpad that caused such behavior. It constantly produced phantom touches even when he was not touching it. This caused BTT to block clicks in some situations. You can check this in BetterTouchTools "Live View"
One other user with a similar issue had a broken usb or bluetooth device connected to his Mac, which caused the bluetooth stack to reset every few miliseconds also resulting in blocked clicks.