Where are my Carthaginian harbours?

Working on that for a while were you?

Free buildings are not the same as the actual building that you purchase or construct. The game creates a copy-cat of the 'real' building, and this copy-cat version is what is given as a free building. The game then handles all the issues of building-class requirements for the next better building in a chain, National Wonder requirements, etc. for the 'free' version of 'real' buildings so that these issues are seamless to the player. As such, since the free building is in many ways not considered to be a 'real' building, you get all the differences and effects mentioned as relates to Carthage's free Harbors. (Free versions of buildings apparently are not 'hooked' to the city animation shown in the main map).

Mod-Makers cannot fix graphic issues because the code for the graphics engine of Civ5 has never been released. IGE can remove and re-assert Fog of War because there are specific commands for that within the game's LUA API -- but the reason IGE cannot re-assert unrevealed tiles in the mini-map when you use IGE to 'Glance at Map' is because of the lack of access to the graphics engine and therefore the code that controls the mini-map.