In the designer, one can see the flasks and colors are correct in the initial setup.

http://www.wargear.net/boards/designer/4791

However, when in the game, I notice that the colors on the flasks don't necessarily match to the controlling nation's colors.  Furthermore, I can view one of the Allied flasks (and I'm playing the Axis).

http://www.wargear.net/games/player/252884

Any thoughts on why this is?

In the Dev game have you Restarted or added new Territories since starting?  If so you may Terminate that one and start a completely new game to ensure everything is picked up. My  quick look at the setup and Rules appear to be set up for what you are wanting.

It looks like it should be right... 4791 is a scenario right, have you checked the scenario settings from the base board aren't doing this?

Right. For the base board, no issues. I think Yertle's suspicion is correct re: adding new territories after the invite. I will term and restart.

That worked. Thanks guys.