To keep this short and simple, I hadn’t used my netbook for a couple of days and it turns out I had installed xbindkeys. Probably in a case to get a key working as a shortcut for something, but never getting beyond actually installing it and creating the default config as the program suggests by running xbindkeys –defaults > ~/.xbindkeysrc. This just happens to enable 3 default keybindings, one of which is Ctrl-F (!?) to open an xterm. It also grabs that shortcut, and it no longer does its usual task in the program you’re running.
It also ignores xkb keyboard layouts, so for me using dvorak that means my Ctrl-U shortcut just disappeared, no more delete line of text in terminal, yay!
Fortunately I worked out that my issue was with Ctrl-F and a google search for that and xterm keyboard shortcut lead me to a where some poor sob had also run into the issue, but had worked out that xbindkeys was the culprit.
I’ve filed a wishlist bug report on the Debian BTS, but I doubt they’ll see it as something worth fixing.