AFTER LNDG ABQ A B737 CREW CROSSED AN INTERSECTING RWY WHILE A SMALL ACFT WAS DEPARTING.

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AFTER LNDG ON RWY 3 IN ABQ; ATC INSTRUCTED US TO 'HOLD SHORT OF RWY 8 ON TXWY CHARLIE FOR LNDG TFC AND STAY WITH ME.' AS I TAXIED UP TO RWY 12; MY FO ASKED ME; 'WE ARE CLRED TO CROSS 12 CORRECT?' AND I REPEATED THE ORIGINAL CLRNC. FO THEN LOOKED RIGHT AND RPTED 'CLR RIGHT' AND I LOOKED LEFT AND RPTED 'CLR LEFT' AND CROSSED RWY 12. JUST AS I CLRED RWY 12 WE HEARD A TRANSMISSION FROM AN UNIDENTIFIED ACFT; 'ABQ TWR I STOPPED MY TKOF BECAUSE AN AIRPLANE CROSSED THE RWY.' AT THIS POINT I LOOKED BACK OVER MY LEFT SHOULDER AND OBSERVED A SMALL; ALL WHITE HOME BUILT ACFT ABOUT 1500 FT UP RWY 12 FROM MY POSITION. ABQ TWR THEN REPEATED THE SAME INSTRUCTIONS TO US AS BEFORE 'HOLD SHORT OF RWY 8.' THERE WAS VERY LITTLE DIALOGUE BTWN ATC AND THE HOME BUILT. WE THEN RECEIVED A CLRNC 'CROSS RWY 8 AND CONTACT GND CTL.' AFTER PARKING AT THE GATE I CALLED THE CTL TWR AND ASKED TO SPEAK TO THE SUPERVISOR. APPROX 2 TO 3 MINS PASSED BEFORE THE CTLR CAME ON THE LINE. I INTRODUCED MYSELF AND ASKED POINT BLANK DID WE OR DID WE NOT HAVE A CLRNC TO CROSS RWY 12. THE CTLR THEN RESPONDED WE ARE CHECKING ON THAT RIGHT NOW. DURING THIS TIME WE BOTH CONVERSED ABOUT THE INCIDENT AND HE STATED 'THE PLAN WAS TO HOLD YOU SHORT OF 12.' HE PUT ME ON HOLD FOR ABOUT A MIN THEN CAME BACK AND STATED; 'YOU HAD A CLRNC TO HOLD SHORT OF RWY 8.' HE THEN ASKED ME IF I HAD A PROB WITH THIS AND IF NOT IT'S OVER; BECAUSE WE ARE NOT GOING TO PURSUE THIS AND THE HOME BUILT PLT IS NOT GOING TO PURSUE THIS. I THEN APOLOGIZED FOR MY PART OF THIS INCIDENT AND SAID GOOD-BYE. UPON ARR IN MDW; I CONTACTED A CHIEF PLT AND I GAVE HIM THE DETAILS OF THIS INCIDENT. HE SAID HE WOULD CALL AN ATC SPECIALIST. I THEN CONTINUED TO FLY THE REST OF MY PAIRING. THE CHIEF PLT LATER LEFT A MSG ON MY HOME PHONE THAT WE WERE CORRECT AND THE INCIDENT DID NOT HAPPEN AS FAR AS ABQ WAS CONCERNED. UNFORTUNATELY IT DID HAPPEN. THE ACFT (HOME BUILT) WAS TAKING OFF ON RWY 12. WHETHER HE HAD A CLRNC OR NOT IS UNKNOWN. WHETHER RWY 12 WAS THE INTENDED RWY IS UNKNOWN. AS I STATED EARLIER THE ACFT WAS A SMALL 2 SEAT HOME BUILT ABOUT THE SIZE OF AN RV4. AT THE POINT I FINALLY DID SEE HIM; I DID NOTICE A WING TIP STROBE AS THE ONLY VISIBLE LIGHT ON. I BELIEVE THE CONTRAST BTWN THE LIGHT COLORED CONCRETE RWY AND THE ALL WHITE ACFT MADE HIM UNDETECTABLE AS I APCHED THE RWY. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: RPTR STATED HE WAS FIRST AWARE OF THE DEPARTING LIGHT ACFT WHEN THE PLT NOTIFIED THE TWR HE WAS STOPPING HIS TKOF BECAUSE OF THE AIRLINER XING THE RWY. THE RPTR LOOKED BACK AND SAW THE LIGHT ACFT'S STROBE LIGHTS ABOUT 1500 FT AWAY ON THE RWY. HE SAID EVEN THOUGH IT WAS BROAD DAYLIGHT WITH 50 MILES VISIBILITY; IT WAS DIFFICULT TO SEE THE SMALL 2 SEAT ACFT. HE SAID THE RWY IS BLEACHED WHITE CEMENT AND THE SMALL ACFT WAS PAINTED WHITE. HE SAID THEY WERE HELD SHORT OF RWY 08 BECAUSE A FORMATION OF MIL F-18'S WERE LNDG AT THE TIME. AFTER PARKING; THE RPTR TALKED TO THE CTLR THAT WAS WORKING THE LCL CTL POSITION AT THE TIME OF THE INCIDENT. THE CTLR SAID HIS PLAN WAS TO HOLD THE FLT SHORT OF THE XING RWY UNTIL THE SMALL ACFT DEPARTED.