RWY TRANSGRESSION. ACFT TAXIED ON RWY WITHOUT CLRNC.

Narrative

OUR ACFT WAS CLRED ONTO RWY 28 TO HOLD SHORT OF RWY 23L. RWY 28 WAS ALSO BEING USED FOR TKOF. CLRNC WAS READ BACK BY FO. CAPT CALLED FOR BEFORE TKOF CHKLIST. THE ACFT WAS STOPPED ON RWY 28. CAPT AND FO NOTICED EMB-120 CROSS THRESHOLD AND LAND ON RWY 23L. CAPT THEN TAXIED ONTO RWY 23L. CAPT AND FO BOTH NOTICED B-737 ON FINAL AND MADE MENTION OF IT. FO THEN ASKED IF FLT WAS CLRED FOR TKOF. TWR ADVISED THAT FLT HAD NOT BEEN CLRED ONTO RWY 23L. TWR TOLD B-737 TO GAR AND LATER CLRED FOR TKOF. BOTH CAPT AND FO THOUGHT FLT WAS CLRED INTO POS RWY 23L AND ACKNOWLEDGED BY FO. BUT FLT WAS NOT CLRED ONTO RWY 23L. SOMEHOW; WITH THE CLRNC INTO POS ON RWY 28 TO HOLD SHORT OF RWY 23L AND THE BEFORE TKOF CHKLIST; CONFUSION RESULTED AND THE FLT TAXIED ONTO RWY 23L WITHOUT CLRNC. I THINK THERE ARE 2 PROB AREAS. 1) I WOULD RECOMMEND THAT NO CLRNCS ONTO ONE ACTIVE RWY TO HOLD SHORT OF ANOTHER ACTIVE RWY BE GIVEN. THIS PUTS CREW INTO PRECARIOUS SIT WHERE THEY ARE NOT ON TXWY AND THEY ARE NOT ON THE ACTIVE RWY FOR TKOF. 2) I WOULD RECOMMEND OUR AIRLINE CHANGE THEIR BEFORE TKOF CHKLIST. I RECOMMEND INSTEAD OF PA FOR FLT ATTENDANTS TO BE SEATED; 2 CHIMES BE GIVEN. IT WOULD TAKE LESS TIME AND FO WOULD NOT BE REMOVED FROM LOOP AT THIS CRITICAL TIME. I HAVE GIVEN CONSIDERABLE THOUGHT AS TO WHAT MIGHT HAVE BEEN SAID TO CAUSE CONFUSION AND NOTHING CAN BE VERIFIED; IE; ANOTHER ACFT CLRNC TO HOLD OR LNDG CLRNC. SOMETHING MUST HAVE CUED US BUT WE HAVE NO PROOF.