TKOF ABORTED BY AN A319 FLT CREW AFTER RECEIVING AN ECAM MESSAGE RELATED TO A NAV DISCREPANCY BECAUSE OF THE WRONG RWY SELECTION IN THEIR FMG'S AT PHL; PA.

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DURING PREFLT WHEN ALIGNING THE IRU'S; IRU #1 SHOWED FAULT. AFTER TRYING TO SHUT OFF THE IRU'S AND INITIALIZE AGAIN; THE FAULT REMAINED. CONTACTED MAINT WHO DIRECTED US TO TRY AGAIN AND PULL THE APPROPRIATE CIRCUIT BREAKERS. THIS ALSO RESULTED IN A FAULT. OUR MAINT PERSONNEL WERE THEN CONTACTED AND A DISCREPANCY WAS ENTERED IN THE LOGBOOK. THE TECHNICIAN TRIED ANOTHER ALIGNMENT AND THIS ONE WORKED. HOWEVER; MAINT CTL AND THE TECHNICIAN NOTED THIS ACFT HAD A RECENT HISTORY OF PROBS WITH IRU #2. SINCE IRU #1 NOW HAD A PROB; THERE WAS CONCERN ABOUT A SOFTWARE PROB. A SYS TEST WAS PERFORMED ON ALL 3 IRU'S. TEST WAS GOOD. LOGBOOK WAS COMPLETED AND BASED ON THE HISTORY; THE ACFT WAS DOWNGRADED TO CATI AND THE FLT RELEASE WAS AMENDED. FLOWS; BRIEFING; AND CHKLIST WERE ACCOMPLISHED. THE RELEASE SHOWED RWY 27L AND THE ATIS RPTED RWY 9L IN USE. TKOF CARD AND BRIEFING WERE BASED ON RWY 9L. WT AND BAL WERE CORRECTED FOR RWY 9L AND PAX COUNT (REMOVE 1 INFANT). PUSH WAS ACCOMPLISHED 45 MINS LATE. TAXI WAS NORMAL AND TKOF STARTED WITH FO FLYING. AT 80 KTS; ECAM SHOWED 'NAV DISCREPANCY/CHK ACFT POS.' BASED ON THE HISTORY OF THESE NAV SYS; I DID NOT FEEL COMFORTABLE. AN ABORT FOLLOWING COMPANY PROCS WAS ACCOMPLISHED. CONTACTED THE DISPATCHER AND ADVISED THEM WE HAD A REJECTED TKOF AND REQUESTED MAINT CTL. WE THEN REALIZED WE STILL HAD RWY 27L IN THE FMGC. ADVISED MAINT WHAT HAD TRANSPIRED. THEY AGREED THE IRU'S WERE OK. WE COORDINATED WITH BOTH DISPATCH AND MAINT TO INSURE TEMP LIMITATIONS; ACFT OPERATING PROCS; MINIMUM FUEL REQUIREMENTS; AND COMPANY POLICY WERE ALL SATISFIED. SUBSEQUENT TKOF AND ENRTE AND ARR WERE ALL NORMAL. THE IMPORTANT THING I GOT FROM THIS IS; ONCE AGAIN; CHK THE FMGC CAREFULLY. AS WHAT HAPPENS OFTEN WHEN THERE IS MORE THAN 1 ISSUE GOING ON; IT IS EASY TO OVERLOOK 1 ITEM WHEN TRYING TO COVER MAINT ISSUES.