Date: 201203
Local time of day: 1201-1800
Location: ZZZ.Airport, US
Aircraft: Regional Jet CL65; Undifferentiated or Other Model
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Flight phase: Taxi
ATC / advisory: Tower ZZZ
Reporter organization: Government
Reporter function: Local
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Communication Breakdown
Anomaly: ATC Issue All Types; Deviation / Discrepancy - Procedural Clearance
Detector: Person Air Traffic Control
Result: Air Traffic Control Issued New Clearance
Contributing factors: Human Factors; Procedure
Primary problem: Procedure

Narrative: I was working Local Control North at ZZZ Tower. The Ground Controller had been experiencing intermittent problems with his headset and asked me if I could take his frequencies (Ground; Clearance; and Flight Data) while he tried to fix the problem; I took the briefing and tuned the appropriate frequencies. At that time the CRJ advised that he was ready to taxi. I identified myself as `Ground and taxied him to Runway 6. As he was coming up to the runway I told him to turn left heading 040 and cleared him for take off to which he responded with the appropriate heading and clearance. Shortly before this transmission I instructed Mooney; who was in the pattern doing touch and go's on Runway 35; to make a 270 degree turn on final to allow the CRJ to depart; feeling that I should not delay an airliner for a practice VFR aircraft. After clearing the CRJ; I looked back to see the Mooney's progress. I then turned back to the CRJ and saw that he had taxied onto the runway but was not moving. I instructed him to expedite his take off roll due to aircraft on a 2 mile final. The CRJ did not respond. I advised him two more times with no response. I then told him to cancel his take off clearance and hold position. There was still no response and at this time he began his take off roll. I told the Mooney to go around and re-enter the right traffic pattern for Runway 35. The Mooney made the turn approximately 1/2 mile south of the 35 threshold. When the CRJ became airborne; they inquired about their initial altitude. I advised him on this and asked if he had heard my instructions to expedite his take off roll and he said he did not. I then advised him to contact departure. The Mooney came back in and landed without incident. No loss of separation occurred. Later the CRJ pilot called the Tower and discussed the incident with me on the non-recorded line. He told me they were having some mechanical issues and were running through checklists and may not have heard the instruction. However; he also thought there was confusion as I cleared him for take off without telling him to switch frequencies from Ground to Local. I understand where the confusion might lie; although I was still transmitting on all frequencies to the best of my knowledge. I would advise controllers in a situation that has anything unusual to pay extra close attention to what is going on. The likelihood for confusion and error increases; not just on the controllers' part; but the pilot's as well. I understand how they may have been confused; and recognize that I could have been more explicit about remaining on my frequency. However; it is still up to us to keep the situation safe even when something is taking place which we do not expect.


Second narrative: [Narative #2 had no additional information.]


Synopsis: Tower Controller; working all frequencies temporarily due to headset problems; described a confused takeoff clearance event when an air carrier failed to depart as instructed.