Catcher in catcher's box prior to LBR?

[DaveASA/FED]

Ok here is how it was asked to me.
Live ball, R1 on 3rd R2 on 2nd (rounded the bases) ball thrown back to pitcher in circle runners head back to bases. Catcher and infielders head to circle to talk to pitcher, not asking for time. R1 takes off and scores and R2 advances to 3rd. What is the call??

The guy describing this to me wanted umpire to call time and send the runners back. My thought was runners are out for leaving early, he stated that the book says that you can't call leaving early unless the catcher is in the catchers box ready to recieve a pitch. The only time I remember reading the catcher needing to be in the box is for the pitcher being ready to pitch, and requesting the batter to enter the box.

Am I missing something or is he mixing rules??? By the way the call on the field in this game was that the runners advance was allowed run scored and now R2 is on 3rd.