The system recognizes the coding for each realm, and that's how the guards differentiate between the sides. Otherwise, if you were to go into the PvP/ pk state, during the off time between RvRs on the bridges, you'd be targeted as well. I'm not entirely certain as to whether or not a patch was applied to the guards to make them non hostile during the off time (as I have stayed well away from the evene bridge since I last tried to use ruemon as a shortcut and was promptly killed by the eos guards) but it is possible, that if such were the case, the coding isn't recognizing the switch between active rvr and inactive times.
But then again I have not been on since Monday, so maybe you've all resolved it?
I would like to give fatal and his sms some props for farming guards though (not sure if it was fatal group or not) but still, I am bemused by the notion still.