Is it only happening in Lvl synch dungeons? Because any time I'm level synched as a Summoner or Scholar my Aetherflow stacks are reset and I have to use it again. (As long as the Egi's level reque is met it'll stay out though, and eos just stays out in general)

Other wise I don't know. I don't think iLvl sync negates it unless there's a lvl 51-60 trait that allows a 4th stack. (I've neglected my alt classes since 3.0 so I don't know)