I'm quite stumped as to why isn't it working for you with a keyboard. (Directional key + high profile) pressed together gives running. Press a third key with these two, the legs key (all three pressed together) and you get free running.
Edit:
You might want to try and map the 'legs' to something other than the space key. Just a suggestion, since space-bar sometimes does not work properly for me in games.
Also Assassins Creed games take a heavy toll on your RMB, due to the constant need for high profile mode...mine is pretty unresponsive now-a-days.
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