The rules for when flying pay starts have changed regularly in the last 15 years or so. In the early 90's when long holds were common in between bits of flying training the paymasters realised the rules had changed so it was 72 weeks of flying training instead of 72 weeks from the start of flying training. As a result a number of people who had already started receiving flying pay had it stopped!
I was one of the ones affected, but after appealling I had it reinstated. The reason - my terms of service were the ones in force when I joined in 1987, and predated the rule change. Sounds pretty much the same as the position you're in.
It took 14months of arguments, but resulted in a nice lump sum back payment and I started middle rate etc earlier than I otherwise would. Worth the effort.