Keyboard controls seems to either work as intended or not work at all. As I said in the original post they did not work at all when I tested them at GameJolt and NewGrounds. I saw nothing wrong when testing on itch.io, but I did not test full screen mode. When I went back and tested switching to full screen mode, the result was at the controls stopped working. When switching back, the controls still didn't work. So I have turned of the full screen possibility in itch.io.
My best hypothesis is that there is something in the code surrounding the game on the page in the different cases that interferes with the controls, but I'm completely out off my depth on what that could be.
If ct.js is something for me? On that the jury is still out.