We've just released the updated EF3 plugin 3.12 version. Check if you experienced the fixed problem.
After saving EF3 settings for your template the modifications keeps disppearing after some time.
After saving the configuration at the template backed, the settings were stored in the custom css file in Joomla cache.
While loading the site, the framework checks if the custom css with all settings exists. If the file exists the framework uses it otherwise the new custom css is created.
Joomla delates all old files from cache folder while loading the site. So while loading the site, at first the framework looked for the custom css file and found it in the Joomla cache directory.
Then Joomla deleted it.
How it looks now?
We moved the custom file to the template cache directory, so the problem will not occur any more.
You can download the new version of EF3 in the download area of your account.