ATX Y LANDED ON OCCUPIED RWY HAD LTSS FROM ACR X. SYS ERROR PLTDEV.

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ACR X CALLED READY FOR DEP RWY 16L. I INSTRUCTED THE ACFT TO TAXI INTO POS AND HOLD ANTICIPATING TKOF CLRNC AFTER A MIL ACFT DEPARTING RWY 16R. BOTH ACFT WERE DEPARTING IFR TO SACRAMENTO DEPS E RADAR SECTOR. AFTER 'RUNNING' THE SEQUENCE DOWN TO E RADAR; I INADVERTENTLY FILED ACR X DEP STRIP. I SUBSEQUENTLY CLRED ATX Y; 8 MI N; TO LAND ON RWY 16L. I WAS DISTRACTED BY A MTR IN THE VFR PATTERN FOR RWY 16R. THE MTR WAS UNABLE TO MAINTAIN VFR CONDITIONS DUE TO A LOW STRATUS LAYER AND WAS REQUESTING INST APCHS. I COORDINATED CLBOUT AND RELEASE WITH W RADAR FOR MTR. SINCE ATX Y WAS SEQUENCED TO THE L RWY BECAUSE OF MTR ON THE R I ATTEMPTED TO CHANGE LNDG RWYS TO RWY 16R BECAUSE I KNOW THAT ATX Y PLTS PREFER RWY 16R. ATX Y SAID HE WAS LINED UP ON THE L 3 MI FINAL AND WOULD GO AHEAD AND LAND ON THE L. UPON SCANNING THE RWY I DID NOT NOTICE ACR X IN TKOF POS. IN RETROSPECT; ACR X'S LIGHTS SEEMED TO BLEND IN WITH THE RWY AND APCH LIGHTS AND THE GND CTL'S BRITE RADAR DISPLAY PARTIALLY BLOCKED MY VIEW OF THE APCH END OF RWY 16L. WHEN I CHKED TO SEE IF ATX Y HAD LANDED AND CLRED THE RWY I SAW ACR X IN TKOF POS. ACR X CALLED AT THAT TIME AND WANTED TO KNOW WHAT WAS GOING ON. AFTER I APOLOGIZED AND GAVE ACR X OUR TELEPHONE NUMBERS; ATX Y TOLD ACR X TO RELAX; HE HAD THEIR ACFT IN SIGHT; WAS CLRED TO LAND AND LANDED. THEY WERE IN NO DANGER. I BELIEVE THE FACTORS WHICH CONTRIBUTED TO THIS OCCURRENCE WERE MY INADVERTENTLY FILING THE DEP STRIP; THE DISTR BY MTR DUE TO MVFR WX CONDITIONS; MY PARTIALLY BLOCKED VIEW OF THE APCH AND HAD I MOVED 1 STEP TO THE R MY VIEW WOULD HAVE BEEN UNOBSTRUCTED AND ATX Y PLT ELECTING TO LAND ON AN OCCUPIED RWY.