It shouldn't be the relic as I've seen it proc without issue while someone was holding it.
Did anyone use a different subclass during the encounter and then swap back near the end? I have had it once on a different raid encounter that it didn't count and the only difference between that run and the successful one was that someone used a different subclass till near the end (even though they swapped back well before the encounter ended).
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No, I don't think that happened because I've done it multiple times and I've had the same problem with the gatekeeper portion.