A 'CARJ' CREW; DEPARTING ROC; LEVEL AT 3000 FT; UNABLE TO CONFIRM CLRNC TO 10000 FT.

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WE DEPARTED ROC TO THE SOUTHWEST WITH CLRNC TO 3000 FT. THE CAPT DID NOT MAKE THE STD NON-FLYING PLT CALL-OUT OF '1000 FT' AGL WHICH IN TURN CAUSED ME TO MISS MY CALL FOR 'FLAPS UP...' THIS HAPPENED AT ABOUT THE SAME TIME TWR HANDED US OFF TO DEP. I THOUGHT DEP CLRED US TO 10000 FT; BUT THE CAPT DID NOT HEAR THE INSTRUCTION. THE CAPT CALLED DEP RIGHT AWAY TO ASK IF OUR FLT HAD BEEN CLRED TO 10000 FT BUT ATC DID NOT RESPOND. THE CAPT THEN CALLED ATC AND TOLD THEM WE WERE AT 3000 FT. ATC'S RESPONSE WAS ONLY 'ROGER.' BY THIS TIME WE HAD LEVELED AT 3000 FT AND HELD THE SPEED BACK TO 200 KIAS BECAUSE THE TKOF FLAPS WERE STILL EXTENDED. THE CAPT STOPPED TRYING TO GET ATC'S ATTENTION AND I KNEW THERE HAD BEEN A MISCOM; SO I KEYED THE MIC AND ASKED IF OUR FLT HAD 'MISSED AN INSTRUCTION.' ATC AND THE CAPT BOTH BECAME DISPLEASED; ATC BECAUSE HE HAD ALREADY CLRED US TO 10000 FT AND THE CAPT BECAUSE HE SAID MY CHOICE OF PHRASEOLOGY WAS EQUIVALENT TO ADMITTING THAT WE HAD MADE A MISTAKE. WELL; BOTH ATC AND THE CAPT WERE IN A WAY CORRECT. BUT ATC TWICE FAILED TO RESPOND CONSTRUCTIVELY TO OUR REQUEST FOR CLARIFICATION AND THE CAPT HAD RESIGNED HIMSELF TO MOTORING ALONG AT 3000 FT FOR I DON'T KNOW HOW LONG BECAUSE HE FELT HE HAD DONE HIS DUTY BY QUERYING ATC. I WAS UNCOMFORTABLE WITH THE IMPASSE AND DECIDED TO MOVE THINGS ALONG. NEXT TIME; I'LL ASK ATC TO 'VERIFY OUR ASSIGNED ALT' SO AS NOT TO IMPLY ANY POSSIBLE WRONG DOING. THE FLAPS WERE RETRACTED AS WE BEGAN CLBING TO 10000 FT. UNTIL THAT POINT I WAS HAPPIER DOING 200 KTS THAN 250 KTS UNTIL THE SIT WAS SORTED OUT. IN THE END I THANKED THE CTLR FOR HIS HELP IN AN EFFORT TO SMOOTH THINGS OVER.