Hello,
I am using Ubuntu 8.04 and noticed that in some applications (notably gnome-terminal) the Ctrl+<key> combos still followed qwerty mappings.

After some searching I stumbled onto a similar thread for dvorak (https://ubuntuforums.org/showthread.php?t=601586). Although the cause has not been yet determined there is a quick way around it: either completely remove the (normal) USA layout or place it after (below) the USA Colemak layout in the gnome keyboard properties.

Note that after doing this I had to use xmodmap -e "remove Lock = BackSpace" (instead of Caps_Lock) to disable caps lock behaviour.

HTH,
Alexandros