I'd tie this together with the Double Move rules. This is not easy to explain, but double walking does not lead the PC to be penalized multiple times based on terrain or enemies. It simply combines both move equivalent actions and applies all penalties at the end of the total action.
Running is a move action, therefore all penalties associated to it should only apply once when you double run.
It the PC were to take a run action, then a standard action, then an action point to run again, someone could argue that the penalties then stack. Personally, I think it is unlikely that the detriments stack as this would be a rather unclear means of writing such a thing.
To put this into real life terms <Which never apply to D&D but are fun to do anyways>, I don't see a discernible difference from running for 6 seconds vs running for 12 seconds prior to attacking.