I wrote a custom configuration section, collection, and element to add/modify to my app.config. All seems to be going well and it works perfectly running in Visual Studio. How
I'm not a fan of using methods in the System.Configuration namespace to write to config files. Reading values using methods in the System.Configuration namespace is never a problem.
Just use LinqToXML instead, at least to check if that is the problem.
I'm guessing your app is installed in C:\Program Data
so while it could be permissions related I suspect the root cause of the System.Configuration.ConfigurationErrorsException: Unable to save config to file
is a lock on the file, use this code to check if that assumption is correct.