I don't know if Ubuntu really did change the settings, or I did sometimes and re-installing the program kept them. Because I actually used the synaptic package manager to remove everything that has to do with codeblocks (installed through software center), and compiled it from source with the latest SVN. That did nothing (except fix broken add-on) because I guess my old codeblocks settings where still saved. Also it is not the first time I got this, before a fresh install of Ubuntu 12.10 and codeblocks from the software center still gave me this problem. SOFTWARE CENTER PROGRAMS ARE BUGGY!
But yes, the problem has been solved, just needed that extra -c.