ON GAR AT BOS RWY 22L; A319 FLT CREW INITIATES EVASIVE ACTION FROM AN EMB135 DEPARTING IN A L TURN OFF RWY 22R. SPLIT LCL CTL FREQS AND TRACON COORD CAUSED CONFLICT DUE TO DELAY IN COORD AMENDED DEP INSTRUCTIONS.

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WE WERE LNDG RWY 22R; DUE TO LNDG TFC NOT CLRING RWY 22L. WE WERE APPROX 100 FT AGL; TWR INSTRUCTED US TO GO AROUND AND FLY RWY HEADING. AT APPROX 500 FT MSL; I SAW A REGIONAL JET CONVERGING FROM ABOVE. WE TOOK EVASIVE ACTION TO AVOID. IN SUBSEQUENT CONVERSATION WITH THE TWR SUPVR; HE INFORMED ME THAT HORIZ SEPARATION HAD BEEN 1200 FT AND VERT SEPARATION 100 FT. CONTRIBUTING FACTOR: 1) REGIONAL JET HAD DEPARTED RWY 22R AT BOS. SID DIRECTS A TURN TO 140 DEGS AFTER TKOF; BRINGING THE ACFT ACROSS THE CTRLINE OF RWY 22L. BOS TWR USES 2 DIFFERENT FREQS FOR CTL OF THESE RWYS; 119.1 FOR RWY 22L AND 128.8 FOR RWY 22R. THE CTLR DELAYED HIS INSTRUCTION FOR THE REGIONAL JET TO TURN R FOR 12 SECONDS; CAUSING THE RJ TO CROSS OUR PATH. MY SITUATIONAL AWARENESS WAS COMPROMISED BECAUSE I DID NOT KNOW TFC WAS DEPARTING RWY 22R AS WE WENT AROUND BECAUSE HE WAS ON A DIFFERENT FREQ. 2) FOR SOME REASON; EITHER PLT ERROR OR ACFT MALFUNCTION; GAR MODE WAS NEVER ACHIEVED WITH THE FLT MGMNT GUIDANCE COMPUTER OF OUR ACFT. THIS CREATED A HAZARDOUS SIT IN AND OF ITSELF. UPON LNDG GEAR RETRACTION; A MASTER WARNING ALARM SOUNDED WITH ACCOMPANYING FLASHING RED LIGHT. THIS OCCURRED AT APPROX 300 FT MSL; JUST BEFORE I SAW THE CONFLICT WITH THE RJ; DUE TO THE FACT THAT THE ACFT WAS STILL IN THE LAND MODE AND THOUGHT IT WAS GOING TO LAND WITH THE GEAR UP. THIS FURTHER COMPROMISED MY SITUATIONAL AWARENESS TO THE POINT WHERE I FEEL IT WAS EXTREMELY FORTUNATE THAT THIS DID NOT RESULT IN A SERIOUS ACCIDENT. AS TO WHY GAR MODE WAS NOT ACHIEVED; WHEN TWR INSTRUCTED A GAR; I ACKNOWLEDGED AND ANTICIPATED THE FO'S (THE PF) REQUIRED CALLOUT OF 'GAR; TOGA.' HE DID NOT MAKE THE CALLOUT; SO I PROMPTED HIM WITH 'GAR; TOGA.' HE RESPONDED BY ESTABLISHING A CLB ATTITUDE AND PUSHED THE THRUST LEVERS FORWARD. WE BOTH FAILED TO VERIFY THAT TOGA WAS ANUNCIATED ON THE FLT MODE ANNUNCIATOR. I WAS LOOKING AT THE FLAP HANDLE AND PROMPTING HIM TO CALL FOR GAR FLAPS; WHICH HE HAD FAILED TO DO. THE FO CONTENDS THAT HE DID INDEED SELECT TOGA WITH THE THRUST LEVERS. I STRONGLY SUSPECT THAT GAR MODE WAS NOT ACHIEVED BECAUSE OF HIS FAILURE TO SELECT TOGA WITH THE THRUST LEVERS. OUR (WITH A STRONG EMPHASIS ON 'MY') FAILURE TO VERIFY THAT TOGA HAD BEEN ACHIEVED WAS AS LARGE A FACTOR AS THE DELAY IN THE TWR INSTRUCTING THE RJ TO TURN. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: THE CAPT STATED THAT AS HE WAS DETERMINING THE REASON FOR THE MASTER CAUTION LIGHT; THE FO WAS INITIATING A TURN TO AVOID THE DEPARTING ERJ-135 XING IN FRONT OF THEM. IT WAS IN THE EVASIVE MANEUVER THAT ATC ASKED IF THEY WERE PROVIDING VISUAL SEPARATION FROM THE ERJ-135. RPTR STATED THAT HE RECOGNIZED THE OPERATIONAL NECESSITY FOR SPLIT LCL CTL FREQS; BUT THIS INCIDENT SHOWED THE PRINCIPLE FLAW IN THAT TYPE OP -- TIMELY AND EFFICIENT INTRAFAC COORD.