ATCT LCL CTLR MISSES B1900 ACFT ENTERING THE ACTIVE RWY. A319 TKOF CLRNC CANCELED BY THE LCL CTLR AT PVD.

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A319 ON RWY 5R IN POS. XING RWYS IN USE FOR BOTH ARRS AND DEPS. ANOTHER ACFT (C403) LANDED RWY 34. A319 CLRED FOR TKOF. PLT RESPONDED 'SOMEONE ON THE RWY.' THINKING IT'S THE CESSNA OFF RWY 34; I LOOKED MIDFIELD AND CANCELED TKOF CLRNC; TOLD THE A319 THE TFC WAS CLR OF THE RWY. AS THE A319 RESPONDED AGAIN WITH 'SOMEONE ON RWY;' I SAW LIGHTS FROM THE B1900 ON RWY 5R. THE B1900 MISSED HIS TAXI RTE AND HOLD SHORT INSTRUCTIONS. AS NUMEROUS ACFT HAD BEEN TAXIED TO RWY 5R ALL EVENING; I HAD NO REASON TO NOTICE THAT ACFT (B1900) APCHING RWY 5R; FULLY EXPECTING IT TO TURN AT TXWY PRIOR TO THE RWY. MY ATTN WAS DRAWN TO THE C402 EXITING RWY 34 JUST PAST THE RWY INTXN. OTHER DISTRS INVOLVED: THE C402 RPTED TXWY SIGN 'INOP;' WHICH LED ME TO QUESTION HIS EXITING AT THE TXWY OR ONTO RWY 5R. NUMEROUS 'DSP/EDCT' TIMES TO BE MET. MUCH COORD WITH DEP. THE A319 HAD HIS DSP RUN OUT AND HAD TO RE-COORD A DEP TIME FOR THEM. COORD WITH THE DEP CTLR FOR RELEASE OF THE A319 INCLUDED TFC FROM WHICH I WAS TO VISUALLY SEPARATE. MUCH COORD WITH GND FOR XING OF RWYS OF BOTH INBOUND AND OUTBOUND ACFT. A POSSIBLE FACTOR WAS THE INTXN AT WHICH THE B1900 ENTERED THE RWY 5R MAY HAVE BEEN BLOCKED BY THE SUPPORT PILLAR FOR TWR WINDOW. HOWEVER; THIS USUALLY IS AVOIDED BY SIMPLY MOVING SLIGHTLY WHEN YOU SCAN. THE MAIN DISTR WAS THE C402 LNDG -- FOR ME TO VISUALLY ENSURE THEM CLR OF RWY 5R. THEN THEY RPTED THE TXWY SIGN INOP; DRAWING MY ATTN AGAIN TO THEM. AND SINCE THE B1900 WAS ON A TAXI RTE THAT IS ROUTINELY USED FOR RWY 5R; I HAD NO NEED TO THINK THE LIGHTS COMING TOWARD THE RWY WOULD NOT TURN TO PARALLEL THAT RWY. THE 3 CTLRS IN THE TWR ALSO DON'T RECALL SEEING THE LNDG LIGHT ON THE B1900; IT MIGHT HAVE MADE THE ACFT EASIER TO SEE AT THE EDGE OF THE RWY.