Forget hidden part. Read again what you said and mapped Windows button to 'something'. Now everythings working fine!
Please try the 3.4.1.4 update and report how it works. Should be working without the need to configure keys.
The previous handling was not preserving the original key events why the meta state could be lost.
The original code made some attempts for that, but the events were lost. I modified this handling, even if it probably means that my changes will be harder to merge to the original.
The initial changes was fine, but the code was too messy so I rewrote the handling again, took quite some time...
If the changes work fine for other users, I will post in the original thread again, these changes probably addresses most of the problems with unwanted changes that the module introduces.