After setting up all the preferences, make a copy of the preferences xml file.
Then, if it happens again, it's a very quick fix to restore the file
The trick of setting preferences, then copying uspreferences206.xml to the act directory as preferences.xml works great.
uspreferences206.xml is in documents and settings\username\application data\act\act for windows 9\preferences
*replace us for eu or au if not in North America
You should copy it to c:\program files\act\act for windows\preferences.xml
* Keep a copy of the original preferences.xml file incase you have a problem
These paths assume act 9, and defaults locations, the concept is the same for other versions. What this does is, when the preferences blow up, act reads the preferences.xml from it's directory, but since they are all set, everything works normally. The one caveat is, the first time you open act after the preferences die, addons will not load, but all subsequent loads work fine.
Note: this won't save customized menus/toolbars, but will keep email and word processor, etc settings. The menus/toolbars can be backed up seperately