1/16: Received email from FSO stating “You were granted Secret eligibility on 01-16-2019, but the government system has not updated to reflect the new access.”
2/7: My FSO hasn’t been able to see the “new access”
What could be holding this up?
Let me guess: this is not for DoD, so we are not talking about JPAS here, otherwise the email notification to the FSO would have been sent out at the same time as the system was updated.
Or maybe not. Maybe the FSO got a phone call from their POC and they’re waiting for it to update in JPAS.
Or something else entirely.
Glad I could be of help 
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DoD contractor. My FSO called whatever organization that performs the investigation/adjudication and received the info that I was granted secret eligibility.
It would make sense that they are waiting for it to update in JPAS, but 3 weeks seems like a long time for that update to happen.
By any chance, is your clearance the result of a denial followed by an appeal which you won? The update in JPAS could be delayed to give the government time to appeal the decision in your appeal.
Good thought, no denials so far in the process. Interim was granted fairly quickly (within 3 weeks of submission). Phone Interview was 7 weeks later.