To reproduce, create a non-core pointer/keyboard pair and assign your mouse/keyboard to it:

xinput list  # note the id numbers for your keyboard/mouse
xinput create-master test
xinput reattach <mouse-id> "test pointer"
xinput reattach <keyboard-id> "test keyboard"

Note that your mouse will have a new cursor independent from the other one (which may remain visible).

Then click in any Qt application and try typing using modifier keys (eg, Shift). Despite pressing Shift, everything will be lowercase (because Qt is checking the core keyboard's Shift state, not the state for your "test keyboard"). Similarly, if you assign a keymapping to your keyboard device (xkbcomp with the -d option), it will be ignored and the core keyboard's mapping used instead.

To restore your system back to normal:

xinput reattach <mouse-id> "Virtual core pointer"
xinput reattach <keyboard-id> "Virtual core keyboard"
xinput remove-master "test keyboard"