Try manually deleting your settings files. They should be here in XP:
C:\Documents and Settings\YOUR_USER_NAME\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Setting
You may need to turn on hidden files/folders in explorer first. The main files are user.setting/diplomacy.user.setting and camera.setting/diplomacy.camera.setting
When you run the game again, it should recreate them with defaults, but if there was something wrong with the files before, they should save properly now.