GND CTLR STOPPED ACFT JUST PRIOR TO RWY INCURSION; FLC CONFUSION ON TAXI DIRECTIONS AND RWY IN USE.

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WE WERE PARKED ON THE E RAMP AT DUPAGE; IL ARPT (DPA) AND CALLED FOR TAXI AND IFR CLRNC TO CHICAGO-MEIGS (CGX). GND CTL RESPONDED 'YOUR CHOICE OF RWYS; WIND 060 DEGS AT 10 KTS.' THE PNF RESPONDED 'WELL WE DON'T WANT THE SHORT ONE; AH; ---15-33. WE WILL TAKE WHICHEVER ONE IS CONVENIENT FOR YOU -- AH; RUNWAY 1 OR; AH; 10-28.'GND IMMEDIATELY RESPONDED 'ROGER TAXI TO RWY 10; WIND (DIRECTION AND SPD).' WE HAD JUST LANDED ON RWY 1L; 25 MINS BEFORE AND HAD USED RWY 19R 2 DAYS BEFORE AND I WAS 'PRIMED' TO 'HEAR' RWY '1' SOMETHING (L OR R) IN THIS CLRNC. WELL; WHAT I WASN'T PRIMED TO HEAR WAS RWY 10. THE PNF AND I DID NOT VOCALLY CONFIRM THE TAXI CLRNC (WE FLY TOGETHER EXCLUSIVELY AS A CORPORATE FLT CREW 25 HRS PER MONTH). AS WE ENTERED A 'RAT-MAZE' SET OF TXWYS ON THE E SIDE OF THE ARPT; THE GND CTLR CALLED 'I HAVE YOUR IFR CLRNC WHEN READY TO COPY.' THE PNF RESPONDED 'READY TO COPY' AND THE CTLR BEGAN TO IMMEDIATELY ISSUE THE CLRNC AND OF COURSE IT WAS DIFFERENT THAN 'CLRED AS FILED.' THIS DIVERTED THE PNF'S ATTN FROM THE TAXI MAP OF THE ARPT AND PREVENTED HIS NORMAL DUTY OF FOLLOWING TAXI PROGRESS ON THE ARPT DIAGRAM. THIS ALLOWED ME TO TAXI USING A RTE THAT WOULD CROSS THE RWY WE WERE CLRED TO TAXI TO. IT IS OUR COCKPIT RESOURCE MGMNT POLICY FOR BOTH PLTS TO CLR (L AND R) ALL RWYS WE TAXI ACROSS; SO WHEN I ASKED CLR R? THE PNF LOOKED UP AND SAW WE WERE APCHING OUR ASSIGNED RWY AND AT THE SAME TIME THE GND CTLR SAW THE SIT AND RADIOED 'HOLD YOUR POS!!' I BRAKED AND STOPPED SHORT OF THE RWY. THIS WAS A CASE OF HEARING WHAT YOU THOUGHT YOU WOULD. BUT OUR COCKPIT RESOURCE MGMNT BROKE DOWN BY NOT DISCUSSING THE TAXI CLRNC AND ALLOWED A POTENTIAL CONFLICT.