@Cowsquack You could also try editing DyalogAltUS.keylayout and putting ⌺ on a different key (and a different glyph on Alt+Shift+`) to see if it is the character or the key combo which is problematic. Maybe some other program listens and captures that combo?
I'm starting to think there is something wrong with my device, I tried editing the keyboard using a keyboard editor, added the stencil to Alt+Shift+`, but it borks