ACR X TCASII RA CLBED INTO AND HAD LTSS FROM MIL Y. SYS ERROR PLTDEV.

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THE PROB AROSE WHEN ACR X; A B727; WAS INBOUND TO ATLANTA ON THE ROME ARR. THE SECOND ACFT MIL Y; AN F16; WAS FLYING FROM TYS DIRECT VU2 AT FL260. ANOTHER CTLR DSNDED Y TO FL230. REALIZING Y WAS IN CONFLICT WITH X; THAT CTLR CLBED Y TO FL250. AT THE SAME TIME; I DSNDED X TO 130. X ACKNOWLEDGED. THEN ASKED IF I HAD TFC FOR HIM. I RESPONDED AFFIRMATIVE THAT TFC WAS AN F-16 AND ABOVE HIM. UPON FURTHER CONVERSATION; X RESPONDED TO A RA TO CLB. X WENT FROM APPROX FL235 UP TO FL247 (APPROX). Y APPARENTLY HAD GONE FROM FL235 TO FL250. X SAID AT FIRST; TCASII SAID TO STAY LEVEL SHOWING TARGET A FL235; THEN TCASII SAID TO CLB. IT WAS A STRANGE SIT THAT TCASII DID NOT INTERPRET THE DATA IN THE CORRECT MANNER. ACTUALLY ADVISING X TO CLB INTO THE TFC. X DID OBTAIN VISUAL CONTACT OF Y FLYING 'OVER THE TOP OF HIM. I THINK THAT THE TCASII DID NOT REACT QUICK ENOUGH; OR WAS EITHER UNABLE TO FIGURE OUT WHAT Y WAS DOING. SUPPLEMENTAL INFO FROM ACN 277961: IN THE VICINITY OF RMG 285 RADIAL (WE HAD BEEN CLRED TO DEVIATE) AND ABOUT 3- NM W OF RMG WE REACHED OUR COMPANY DSCNT PROFILE AND STARTED DOWN FROM FL240. WE SHORTLY RECEIVED A 'TFC; TFC' ALERT FROM OUR TCASII AND WITH THE TFC ALT SHOWING BELOW US (ABOUT FL235) WE STARTED TO DECREASE OUR RATE OF DSCNT. AT APPROX FL235 WE RECEIVED A 'CLB; CLB' COMMAND FROM OUR TCASII; PWR WAS ADDED AND A CLB WAS INITIATED. AT ABOUT FL245 THE FO AND SO SAW AN F-16 PASS OVERHEAD AND TO THE L OF OUR ACFT. WE HAD NOT HEARD ANY RADIO XMISSIONS TO OTHER ACFT IN OUR VICINITY AND AT NO TIME RECEIVED ANY TFC INFO ABOUT THE F-16 FROM ZTL. WE TOLD ZTL ABOUT WHAT HAD HAPPENED; AND THAT WE HAD RESPONDED TO A TCASII RA. ATLANTA SAID THAT THE ACFT WAS AT FL250 AND LATER ACKNOWLEDGED A TCASII RA. QUALITY ASSURANCE WAS CALLED MONDAY AND WE WERE TOLD THAT THE F-16 HAD BEEN ON ANOTHER FREQ AND UNDER CTL OF ANOTHER CTLR. THE F-16 HAD BEEN CLRED TO FL230. WHEN THE CTLR NOTICED THE CONFLICT (THE LAST XPONDER ALT RECORDED FOR THE F-16 WAS FL250) THE F- 16 WAS INSTRUCTED TO MAINTAIN FL250. THE F-16 LATER RPTED THAT HE HAD DSNDED AS FAR AS FL235 AND CLBED BACK TO FL250. WITH THE F-16 BEING A MIL ACFT AND NOT HAVING TCASII FOR OUR TCASII TO CO-ORDINATE WITH; OUR TCASII COULD ONLY USE HIS LATEST XPONDER ALT RECEIVED TO CALCULATE THE BEST COURSE OF ACTION.