MD83 ACFT TAXIING WAS CLRED TO TAXI TO THE RWY AND WHEN THE FLC QUESTIONED GND CTLR IF THEY WERE CLRED ACROSS THE PARALLEL RWY; RPTR CAPT SAYS THE CTLR WAS SNAPPY IN HIS REPLY. THEN THE NEW FO CHANGED TO TWR FREQ BEFORE REACHING THEIR RWY. THE TXWY CROSSES THE RWY AND THEN BACK TO THE TKOF END SO FLC CROSSED THE ACTIVE RWY WITHOUT CLRNC. TWR CTLR ASKED IF THEY WERE ON TXWY WHEN THEY HAD ALREADY CROSSED THE RWY.

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I WAS THE CAPT OF A FLT FROM RNO TO SJC; FLYING AN MD83. I WAS PAIRED WITH A NEW FO; FLYING OUR FIRST FLT TOGETHER; AND HE INDICATED HE HAD ONLY ABOUT 50 HRS IN THE ACFT. I AM A NEW CAPT; WITH 75 HRS AS PIC; BUT WITH OVER 1100 HRS IN TYPE; ALL AT THIS AIRLINE. DUE TO FLOODING; RWY 16R AT RNO WAS USABLE FOR TKOF 'ONLY FOR OPERATIONAL NECESSITY.' GND CTRL TOLD US TO 'TAXI VIA TXWY A AND TXWY D TO RWY 16L.' BECAUSE THIS WAS NOT A 'NORMAL' RWY FOR US TO USE IN RNO; AS WE ENTERED TXWY D I ASKED THE FO TO VERIFY WITH GND THAT WE WERE CLRED TO CROSS RWY 16R. WHEN HE DID THIS; THE GND CTLR WAS SNAPPY IN HIS REPLY THAT WE WERE CLRED ACROSS. AFTER WE CROSSED RWY 16R; FOR SOME REASON; THE FO SWITCHED FROM GND TO TWR. I SHOULD HAVE CAUGHT THIS; BUT DID NOT. AS WE WERE XING RWY 16L ON TXWY D; TWR ASKED IF WE WERE ON TXWY D. YES; WE WERE; AND WE CROSSED RWY 16L; THE ACTIVE RWY. I SHOULD HAVE KNOWN BETTER THAT THIS WAS NOT WHAT OUR CLRNC HAD BEEN. WE CONTINUED WITH NO COMMENT FROM TWR; BUT I WAS CHAGRINED THAT WITH A DIFFERENT RWY; TAXI RTE; AND NEW FO; I ALLOWED THIS SIT TO DEVELOP.