Keytable cz-lat2-prog, i.e. file /usr/lib/kbd/keymaps/i386/qwerty/cz-lat2-prog.kmap.gz misses definitions for Ctrl-[, Ctrl-], Ctrl-\, ... so it's impossible to use these keys on console. I made a patch for the file (for un-gzipped version of course), available at http://physics.muni.cz/~yeti/download/control-kramle.patch .
Thanks, applied in -31