Why my mission had problems and is now temporarily withdrawn:
The patch Friday introduced a bug. Publishing a mission silently corrupts it (we think your copy is fine, but the published version is hosed). This causes a number of problems, the worst of which is map transitions won't trigger. That's why you guys were in the turbolift and nothing happens; without the corruption you'd have gotten a popup dialog from the Admiral's Flag Lieutenant telling you he was expecting you and to come right up, and then you've had transitioned to his office.
As soon as Cryptic fixes the bug, I'll republish it. The corruption appears to happen every time you publish, without fail, so doing it repeatedly doesn't fix anything.
Foundry's still in beta, so either Cryptic wasn't aware of this problem when they left Friday, or decided beta didn't mean "we fix it this weekend". I suspect it's the former, since there's been no dev post about the issue and they're usually really good about that.