ACFT CLBS 400 FT ABOVE CLRED ALT BECAUSE CLRNC IS MISUNDERSTOOD.

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AFTER TKOF FROM RWY 14L (IAH); DEP TOLD US TO TURN R TO 250 DEGS FOLLOWED BY FURTHER R TURN TO 260 DEGS AND CLB TO 5000 FT. OUT OF 4000 FT THE CAPT CALLED 2 TO GO. HE HAD DIALED 6000 FT INTO THE AWL. COMING UP TO 5000 FT I HEARD DEP CALL TFC AT 2 O'CLOCK AND 8 MI; OPPOSITE DIRECTION AT 6000 FT. I SAW THE TFC APPEAR ON THE TCASII WITH PLUS 800 DENOTED. I IMMEDIATELY INITIATED STOP CLB AND ASKED THE CAPT TO VERIFY 6000 FT; BECAUSE I REMEMBERED BEING CLRED TO 5000 FT. I RETARDED THE THROTTLES TO IDLE AND RETURNED TO 5000 FT. THE ACFT PEAKED ALT AT 5400 FT. AT THE SAME TIME ALL THIS WAS HAPPENING; HOUSTON DEP WAS TELLING US TO DSND TO 5000 FT IMMEDIATELY. AT THE SAME TIME WE WERE GETTING A TA FROM OUR TCASII. UPON RETURNING TO 5000 FT; THE FLT PROGRESSED UNEVENTFULLY. SUPPLEMENTAL INFO FROM ACN 277378: ON DEP FROM IAH WE WERE CLRED TO 4000 FT. SUBSEQUENTLY RECEIVED FURTHER CLRNC TO 6000 FT AND SET ALT IN ALT ALERTER. I BELIEVE I READ BACK 6000 FT. WE WERE ADVISED OF HIGHER TFC BUT DUE TO DISTRS DON'T RECALL HIS ALT. FO WAS FLYING AND NOTICED A SEPARATION ON THAT TFC OF LESS THAN 1000 FT ON TCASII. HE IMMEDIATELY RETURNED FROM 5400-5000 FT. ATC THEN TOLD US TO LEVEL AT 5000 FT BY WHICH TIME WE WERE ALREADY LEVEL. AFTER DISCUSSION BTWN THE CREW; WE REALLY COULDN'T DETERMINE IF WE WERE REALLY CLRED TO 5000 OR 6000 FT. I DID HOWEVER READ BACK 6000 FT AND SET IT IN THE WINDOW. GUESS I WASN'T IN THE LOOP AS WELL AS I SHOULD HAVE BEEN.