My understanding of the supply pact is that it does not give extra supply, so much as it makes your current supply cost less. At least i think thats how it was working. I played a long game with large fleet active, and i had max fleet but it was only costing me like 47% or something. That, or i read the supply pact wrong.

I think I had this bug too, today. Not sure though, because truce among rebells fucked up my used supply every other second. But it appeard that the inital bonus vanished when I researched the next "regular" supply level.