Man, so this is what causes it! What a frustrating bug! We had Chronomancers with bizarrely low boon duration, condition classes with strangely low condition duration, and the works. We always figured out that rejoining the instance fixed it, but never what caused it. Glad to finally be aware of the issue.
/u/CrystalRAID can you please make sure this gets looked at? Thanks. :)
Late reply, but yes we are looking in to this.