This is an ongoing problem. I've had it from day one....
It always starts at the what to build next in a city popup. In previous versions, 1.00 & 1.09, it would happen, I would ALT-TAB out, then back in and it would be OK, after resetting my graphics by changing the AA setting to zero and back again. ( The mini map was always screwed up... )
Now, with 1.52, Once the turn is completed, they come back again 75% of the time.
It happens roughly every 10-15 turns, getting worse as the game progresses. Once past 1800 or so, when the world map is known and religions have spread, the game seems to conflict with itself. This is most noticeable when there's a message on the left of the screen and a menu for the build que on the right both trying to happen at the same time. It seems to drop the messages and the info popups instead of alternating ??? The messages are not always dropped, but there does seem to be a correlation.
As to hovering over the flag, it has no effect. Niether does entering the city window. All popups are dead there too. If I go in and change a graphic setting and back a again, it will restore the popups. If I ALT-TAB, it will restore the popups.
Once I've played for an hour or so, I have to shut the game down and restart it. It gets so jittery I can't look at it anymore.
I have a P4 2.8d, 1 gig ram, X600 256meg ati card, and still have a hard time on any map larger than standard once the whole world map is known.
Happy to answer any questions....