I use Windows and Linux. And I use a custom layout (not Colemak but an AdnW-variant).  On my Linux computers, using a custom layout is not a problem: I have a modified xkb-file, which works flawlessly.

On the Windows machines I use the Portable Keyboard Layout (PKL), which DOES cause trouble:

- most shortcuts do not recognise the new mapping of letters. For instance, my AdnW home row is   RIEAOGDTNSK   In other words, I put the letter R on qwerty A.  But, when I want to "select all", I have to press ctrl and the oldA. 

- but, even weirder: if I press ctrl and the new A (which is on the qwerty F position), Windows does not "see" a ctrl-F, but performs a ctrl-N (new window)  ???

- and yet other times, Windows does nothing, but ignores the shortkey.

So, to summarize, with shortkeys:
- sometimes Windows still sees the old qwerty-key (which I do not want)
- sometimes it performs a different action, not belonging to the old qwerty-key but neither to the new key
- and other times Windows completely ignores the short key.

The behaviour I want would be like Linux does: always use the new key definitions, also when typing shortkey combinations. Any hints ? Where should I look ? Thoughts ?  THANKS