I use urxvt (terminal) under awesome (window manager) and ubuntu (os). In graphical mode, c- set the mark but in text mode it inserts a space. The problem is solved when using gnome-terminal but some other key combinations still does not work. For instance, C-: insert a : in both terminals. I do not know where to look at to correct this behaviour. C-h k (help on key combination) followed by one of these combination shows only the key pressed along ctrl, for instance C- is interpreted as .
As stated in comments, the terminal is probably the cause. I believe that C- should not enter a space at the terminal prompt, which it does here.
I identified this question as being related. This one too.