The concerns over the Mark Two Chinook were chiefly spurious engine failure warnings and overfuelling, an unnamed military pilot told the fatal-accident inquiry at Paisley, Strathclyde.
A particular problem was with the newly introduced aircraft's "fadec" - full-authority digital engine control - which in the case of the engine failure warning system meant that a warning light would go on for 12 seconds even if there was no fault.
In the months leading up to the helicopter's crash into a fog-shrouded hillside in 1994 which killed 25 anti-terrorist officers on a flight from Northern Ireland to Fort George, Inverness, there had been "a number of incidents" involving the Mark Two.
The pilot, who could not be named for security reasons, said test pilots refused to test it for a time, and added: "They could not get the software tested properly."
But the inquiry also heard of a letter from a colonel in the Ministry of Defence procurement executive which confirmed that tests were suspended for a time but which went on to say that it would be an "oversimplification" to say the test pilots refused to fly it. The tests had been halted on airworthiness grounds while a fault was investigated, the letter said.
The pilot agreed under cross-examination that all crews would have known in advance of the problems and concerns, and would have been well-drilled for an emergency.
He also told the inquiry that the Mark Two Chinook had two restrictions on the way it could be flown on the fatal night.
The first was that visual rules applied because an anti-icing stipulation meant it could not make the trip on its instruments as this would take it too high. The anti-icing rule was to prevent ice building up and disrupting the engine airflow.
Another restriction limited the fuel it could carry - giving it fewer diversion options.
The unnamed military pilot told the inquiry that he and colleagues had discussed the anti-icing stipulation "in consider able detail" before the Mark Two Chinook arrived in Northern Ireland on 31 May.
Flight Lieutenant Jonathan Tapper, the pilot on the night of the disaster and one of four crew who also died in the crash, asked a senior officer at RAF Odiham, Hampshire if it was permissible to exceed the 4C limit - but was told "under no circumstances" would it be broken.
Any pilot who broke it would get no backing from the MoD and could be held personally responsibly if any litigation arose.
The Chinook was chosen for the flight because it had sufficient capacity for the trip.
And there was no ban forbidding carrying such a large number of senior security experts from travelling together on a single aircraft, the pilot said.
Nor did regulations covering the carrying of VIPs apply to that flight.
The inquiry continues today.