Either it's night time or that's a bug new to Beta 3.3. I can certainly take a colony and install a new governor in Beta 3.1, then go to the shipyard, store etc.
Perhaps spend a night in the tavern? That resets various things and might put the town back to normal, though I never needed to do that after capturing a colony in Beta 3.1. (If the tavern keeper is also missing then it's definitely a bug!)
Out of interest, how did you change the nationality of the colony? I know two ways. One is to go into the fort by land, find a random civilian, be lucky enough that he's a diplomat, demand the colony's surrender and be lucky enough that he does indeed surrender. The other is to attack by sea, rampage through the fort and town, and end up in front of the governor where you have the options to demand a ransom or say that the colony needs a new governor, which allows you to install the nationality of your choice or take the colony for yourself.