Weird Map Glitch

[R.L-C]

everything works fine, no CTD. But I've just taken Krete from the rebels. the problem is that on the mini map the rebels still control Krete and I now own Byzacena, in africa. I can build and hire units at Kydonia but the land is in rebel hands. It says so when you right click over the island.
what do I do to change this.