Checking my alts really quick, but the mission slots unlock: one base, one for patron, one when you get a second agent. My idea was that they’d special cased Lydia to slow the unlock down slightly (and encourage more people to buy patron). That doesn’t seem to have panned out, my Templar alt has all three unlocked with just Faction Recruit and Lydia… my Dragon seems to have the same bug you have.
I’m running AgentTweaks, and it seems to have not suffered too badly in the patch. There’s some collision occuring with the added mission duration time. (Which is in a silly place anyway). But otherwise it works the same as before. Since the bug is only affecting a single character I doubt it’s the culprit here.
Did you happen to have a crash on that character when opening the agent panel today? I recall that one of my characters did when I got back from my galavanting, but I don’t actually recall which one it was (and because of the mods the report is of limited value. I’m so used to random builds of Cartog doing it that I expect any window I open to possibly crash the game)