A FOKKER 100 FLC MEMBER HAD TO LEAVE THE COCKPIT AND THE REMAINING PLT HAD DIFFICULTY WITH A XING RESTR NEAR PHL.

Narrative

I NEEDED TO VISIT THE LAVATORY. LEFT COCKPIT; BUT THE FOOD SVC CART WAS BLOCKING AISLE; SO I RETURNED TO COCKPIT. CTR THEN CLRED US TO DSND AND CROSS KERNO INTXN AT FL260. VERT MODE WAS 'PROFILE.' I SET AND ARMED FL260 AND STATED 'FL260 SET AND ARMED.' FO (PNF) ANSWERED 'SET AND ARMED.' I PUT A 'SLANT 260' BY KERNO IN THE L MCDU AND NOTED THAT WE HAD A BLUE 'LVL' AT KERNO AND 'TOP OF DSCNT' DISPLAYED ON THE NAV DISPLAY. JUST THEN; THE FLT ATTENDANT INFORMED ME THAT THE AISLE WAS NOW CLR. I LEFT THE COCKPIT SAYING 'YOU'VE GOT IT; BE BACK IN A MIN.' I OBSERVED FO PUT ON OXYGEN MASK AND I HAD NO DOUBT; AT THAT POINT; THAT HE FULLY UNDERSTOOD OUR CLRNC AND THAT THE AUTOFLT SYS WAS SET TO AUTOMATICALLY EXECUTE THE DSCNT ON SCHEDULE. WHILE RETURNING FROM THE LAVATORY; I HEARD ENGS REDUCE IN PWR AND FELT THE PLANE PITCH DOWN (INDICATING TO ME IT HAD STARTED REQUIRED DSCNT). ENTERING COCKPIT; FO WAS ATTEMPTING TO RETURN TO FL290! AND STATED THAT WE HAD BEEN CLRED TO CROSS SOMTO INTXN AT 13000 FT AND THE PLANE HAD STARTED AN IMMEDIATE DSCNT AND HE WAS RETURNING IT TO FL290. I RESUMED CTL; CALLED CTR AND VERIFIED CLRNC TO CROSS SOMTO INTXN AT 13000 FT. I THEN BEGAN AN IMMEDIATE IDLE DSCNT THAT REQUIRED SOME USE OF SPD BRAKES TO CROSS SOMTO INTXN AT 13000 FT. NO CONFLICT WITH OTHER TFC. APPARENTLY THE FO (PF DURING MY COCKPIT ABSENCE) WAS CONFUSED IN THAT HE MISTOOK THE ACFT'S DSCNT AS A REACTION TO HIM DIALING 13000 FT INTO THE ALT WINDOW INSTEAD OF IT ACTUALLY BEING THE SCHEDULED DSCNT TO CROSS KERNO AT FL260. ALSO; COINCIDENTALLY; THE FMS'S WERE IN 'INDEPENDENT OP.' THAT MAY HAVE ADDED TO THE FO'S CONFUSION AS THE 'SLANT 260' I HAD TYPED INTO MY MCDU MAY NOT HAVE 'XTALKED' TO THE FO'S SCREEN. IN RETROSPECT; I SHOULD HAVE BEEN MORE POSITIVE ABOUT STATING OUR SIT AT THE MOMENT I TURNED OVER CTL; OR MAYBE I SHOULD HAVE 'HELD MY WATER' UNTIL WE LANDED!