I have the same problem! I just got finished analyzing some recordings of me to try to find out the cause of this. So far I have two recordings in which both involved me fighting a rogue.
In one video I’m out in the world, 1v1 against a rogue. I stepped through frame by frame to find any sort of condition that wouldn’t allow me to trigger Alter Time again. I wasn’t stunned, silenced, locked out of any school of magic, or anything like that.
In the second video, I’m a flag carrier in Eye of the Storm. Once again, Alter Time fails to trigger despite having no debuffs that would prevent me from doing so. I don’t think 5 stacks of flag-carrier debuff would prevent me from using Alter Time, right?
At first I thought Cauterize somehow interfering, but even if I try to trigger Alter Time before Cauterize, nothing happens.