Ok, i tried installing the patches but nothing has worked, i followed the readme files, but am wondering if i misinterpreted them (i am far from a whizz on these things) any thoughts please mate?
For the patches, assuming you want to install the yitzi one, you unzip the contents of v3.5 (primary patch) in the AC folder and accept to overwrite any files needed (press Yes or Yes to everything or whatever). Then do the same for the sub-versions named 3.5b to 3.5d, one at a time. Then you may want to install PRACX.
You'll find the patches here: http://alphacentauri2.info/index.php?action=downloads;cat=2
When finished, load your game and see if the problem persists. If it does, then you may have to start a new game in case old save files are incompatible with the unofficial patch in some way. Also, you may want to keep the bugged save files in case you want to contact GOG support. I'm afraid i can't offer any more help other than that.