Mr Baker said when he broke the surface he activated his Buoyancy Control Device (BCD), which keeps the diver from sinking again.
He saw Dr Allwright come out of the water then submerge again, apparently under control.
The GP soon surfaced a second time, spat out his breathing regulator and shouted "Help" once, then quickly sank again. A rescue boat was in view but was unable to reach the doctor in time.
His body was recovered but medics could not revive him.
Sheriff Ingles said: "The probabilities are that the BCD was not connected to the supply pipe at the time the dive commenced."
He said this meant the doctor and his 'buddy' must have failed to watch the BCD inflate and deflate when they tested the equipment before the dive.
He added there was conflicting evidence of what supervision and guidance the underwater diving centre at Fort William gave the party.
Mrs Allwright, who lives with the couple's two children Fiona, 18 and Stuart, 19, said last night: "I feel as though I have got some closure now and we can lay him to rest, but it is still a mystery to me what happened on that day.
"Graham was not a very experienced diver but he had all the right qualifications. He had ultimate respect for the water and was well aware of the dangers - I think that is part of what attracted him to it.
"So I would have thought he and his buddy would have checked all the connections on their equipment before the dive.
"I don't blame anyone but I still don't know what happened that night. It sounds like a collection of things went wrong and together they turned out to be fatal."
A coroner's inquest is now expected to be held in Merseyside.
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