I have experienced this, and I'm not sure what causes it. Even after refreshing the wine wrapper it still wouldn't ever work right. In the end the only solution I found was to reinstall from scratch. That has completely solved the problem for me, maybe it'll work for you as well.

Your game save files all exist in ~/Library/Application Support/GOG.com/Sid Meier's Alpha Centauri/, so you shouldn't lose anything by doing this.