My credit score on Navy's website is from March. Although they say they update when they get the info from Equifax, mines has not moved.
Since March, they have unsecured my card and giving me a $1,100 CLI.
Is it worth contacting them to get the update or should I just leave it alone?
Is there a reason to think your credit score would have changed? A credit limit going up would not in itself alter your score. It would only affect your score if you had been reporting a relatively large balance. But if your utilization was low before the CLI, then it will also be low now, and therefore they'd be no score increase resulting from the CLI.
My NFCU score is 45 points lower than the score I am getting from MyFico.
I know that my utilization is much lower now than it was in March.