Solved, I needed to remap the virtual keys, to the proper scancode. Did that manually editing the .klc file, because I found no way to do it in MS Layout Creator. Then I just used the Creator to generate the setup files, from the edited .klc .

Detail by example: I have physically switched the z/y keys on the keyboard I have used MS Keyboard Layout Creator to alter the German keyboard so as to type "z" in scancode location 2C (View this webpage for scancode / virtual key settings by locale) I have named the custom keyboard that matches my physical layout "Deunglish" However because Deunglish started of as a German keyboard the Virtual Key VK_Y is still mapped to scancode location 2C, despite setting this as an English keyboard with Creator. Open the .klc file with Notepad++ (or other editor) and replace "y" (virtual key name) with "z" for scancode 2C. Now you will have two definitions for VK z, assigned to two different scan codes, in this case scancode 15. Change that to y as you did for z. Load the klc file in the MS, verify and Build DLL and setup (If you had been using the keyboard you have just edited, you need to unload and uninstall the previous version first. You will likely need to restart) You have successfully swapped virtual keys and assigned them to positions on the keyboard!

Solved, I needed to remap the virtual keys, to the proper scancode. Did that manually editing the .klc file, because I found no way to do it in MS Layout Creator. Then I just used the Creator to generate the setup files, from the edited .klc .

Detail by example:

1. I have physically switched the z/y keys on the keyboard
2. I have used MS Keyboard Layout Creator to alter the German keyboard so as to type "z" in scancode location 2C (View this webpage for scancode / virtual key settings by locale)
3. I have named the custom keyboard that matches my physical layout "Deunglish" However because Deunglish started of as a German keyboard the Virtual Key VK_Y is still mapped to scancode location 2C, despite setting this as an English keyboard with Creator.
4. Open the Deunglish.klc file with Notepad++ (or other editor) and replace "y" (virtual key name) with "z" for scancode 2C.
5. Now you will have two definitions for VK z, assigned to two different scan codes, in this case scancode 15. Change that to y as you did for z.
6. Load the klc file in the MS, verify and Build DLL and setup (If you had been using the keyboard you have just edited, you need to unload and uninstall the previous version first. You will likely need to restart)

You have successfully swapped virtual keys and assigned them to positions on the keyboard! Do this for all keys that may need proper virtual key name to actual output matching, and/or to set to virtual keys to new scan codes.