After the aircrew of Eastern Flight 254 (a Boeing 727, N8107N) had landed on RWY 22 at night and was slowing, the tower controller (CTLR) instructed them to 'turn right on taxiway Bravo, if able, hold short of RWY 18 and remain this frequency.' The crew of Flight 254 was then understood to ask, 'Alright, is that the first lighted one here?' The CTLR replied, 'Affirmative,' then she cleared PDQ Flight 271 (a Piper PA 31, in position and holding on RWY 18) to takeoff. PDQ Flight 271 was rolling on RWY 18 when the CTLR noted that Eastern Flight 254 was slowly crossing the same runway. The CTLR started to transmit to the Eastern Flight, then she canceled the takeoff clearance for PDQ Flight 271. PDQ Flight 271 passed behind Eastern Flight 254 as it was clearing the runway. The crew of Flight 254 stated that they neither received nor acknowledged the instruction to hold short of RWY 18. When queried by the tower after the incident, an Eastern crewmember replied, 'I'm sorry, we didn't hear you.'