It has happened to me multiple times this year.

I think it might be on legs where First cleared on one of the legs but not the other, so it takes you off the other leg's list as well. But that is speculation on my part.

One phone agent was bewildered, one phone agent just fixed it. A SkyClub agent also fixed it but had no idea why, another SkyClub agent tried to tell me I forgot to check a box during check in (yeah ok).

I am glad I noticed though because a couple times it resulted in upgrades to First at the gate.