CE525 PILOT REPORTS ATTEMPTING TO PICK UP PREVIOUSLY FILED IFR FLIGHT PLAN ENROUTE TO NO AVAIL; THEN RECEIVES TCAS TA AT 16500 FEET.

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I FILED AN IFR FLT PLAN VIA DUATS AT XA45. I DEPARTED MARATHON (MTH) VFR WITH THE INTENTION OF OBTAINING THE IFR CLRNC ONCE AIRBORNE AND AWAY FROM THE MARATHON TFC AREA; WHICH WAS BUSY. I MADE CONTACT WITH ZMA AND REQUESTED THE CLRNC. I WAS ASSIGNED A DISCRETE CODE. THERE WERE SEVERAL OTHER ACFT WHICH DEPARTED BEHIND ME FROM MARATHON (ONE A FALCON 900) WHICH ALSO REQUESTED THEIR CLRNC ONCE AIRBORNE. CTR TOLD THE FALCON THERE WASN'T A FLT PLAN ON FILE AND TO CALL MIAMI RADIO. ABOUT 10 MINS LATER CTR TOLD ME THERE WAS NO FLT PLAN ON FILE FOR ME AND TO CALL MIAMI RADIO. THE AIRPLANE WAS AT 16500 FT ALT NEAR KARTR INTXN AT THAT TIME. I TRIED CALLING MIAMI RADIO AND WAS TOLD TO STAND BY; I WAS #3 AT THAT TIME. I CONTINUED NNW ON A 355 DEG HDG AT 16500 FT AND WAITED. THE FREQ WAS VERY BUSY. I TRAVELED FAR ENOUGH THAT I BEGAN TO RECEIVE SEVERAL XMISSIONS AT THE SAME TIME. I LOOKED AT AN IFR ENRTE CHART AND SELECTED A DIFFERENT FREQ. AS I WAS CALLING ON THE NEW FREQ THE TCAS ISSUED A TFC ALERT. I SAW A REGIONAL CARRIER ACFT DSNDING THROUGH MY ALT ABOUT 2 MI AWAY. I TOOK NO ACTION AS THE ACFT WAS ALREADY THROUGH MY ALT; WAS CONTINUING TO DSND; AND WAS GOING PAST MY FLT PATH. I WAS IN VMC IN COMPLIANCE WITH THE FLT RULES FOR CLASS E AIRSPACE. I WAS AT THE PROPER VFR CRUISING ALT FOR MY DIRECTION OF FLT. I WAS FOLLOWING ATC INSTRUCTIONS; ATTEMPTING TO AIR FILE AN IFR FLT PLAN. I WAS ON A DISCRETE CODE; HOWEVER. I DO NOT KNOW WHAT IF -- IF ANYTHING -- THE REGIONAL ACFT MIGHT HAVE BEEN TOLD AS TO MY PRESENCE. I FEEL THIS SITUATION/'INCIDENT' WAS CAUSED BY A COMS FAILURE IN THE DUATS/ATC SYS. MINE WAS NOT THE ONLY ACFT AFFECTED AND ATTEMPTING TO AIR FILE AN IFR FLT PLAN BECAUSE THE 'SYS' DID NOT HAVE THE FLT PLAN FILED EARLIER. IN MY JUDGEMENT; I DID NOT COMMIT ANY INFRACTIONS; OR VIOLATE ANY RULES. I AM RPTING THIS BECAUSE OF THE COMS FAILURE IN THE DUATS/ATC SYS AND FEEL THAT THESE FAILURES NEED TO BE CHRONICLED; AND ADDRESSED. I AM AN ATP RATED PLT WITH C500; C525S; AND C650 TYPE RATINGS. I WAS OPERATING THIS C525 ACFT SINGLE PLT. I HAVE OVER 9000 HRS OF TURBOJET TIME; OVER 2000 HRS IN TYPE; MOST OF IT SINGLE PLT.