Have you modified the stock installation beyond simple setting changes?
You should be able to:
1. go to Admin Panel -> Settings.
Scroll down to "Email Settings" and set that how you want it to be.
2. go to Admin Panel -> Emails
Click on the email you want to edit.
Set it how you want it to be.
Both of these areas should save this information to the database. If you are getting an error please post it.
If you cannot, you might try re-uploading the distribution files to the site.
