I had this happen on my rogue several times in the past however i think it was due to a mouse issue.
I usually turn with rightclick / mouselook and in doing so if there is a corpse anywhere nearby at all it would tend to break hide via me right clicking some random fatties corpse that has been sitting in a dungeon for weeks.
Not sure if this is the issue or not as I no longer play a rogue and they just did some changes to see invis however it might be worth a shot to try just keyboard turning at least while sneaking
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