This bug is really old.
I noticed it since GalCiv II came out and from the first time I played it.
The bug can also be recreated in Dark Avatar.
It's a little hard to explain so I'll try to do it by explaining how to see it happen:

When colonizing a new planet I choose a tile to build starport, then I choose some other tiles to build other buildings. The next thing I do is buy the starport. Then, I want to start building a new vessel in the newly created starport, so I push the build button (all from the same display). Now, when the starport display is up, I expect to be able to choose which vessel to build and only after I leave that display, I expect the next event to happen (another planet being colonized window, another constructor arriving to it's destination window, etc.).
Instead, when I have turns full of events later in the game, I get the next event window popping ontop of the starport display, preventing me from choosing the vessel I need to build, since when I respond to the new event, the display is changing according to that new event. Only after all event are processed, I need to go to the planets list and search for the newly colonized planets' starport which I left idled and choose what vessel to build.

I hope I explained it clearly.
Hope also to see it fixed.

Thanks for your time SD team.

EDIT:
The bug was fixed in Dark Avatar 1.8d