When run for the first time, Mahogany creates a directory called .M in the user's home directory. The file $HOME/.M/config will contain the current program configuration for this user. Only values different from the default configuration are stored here. If you want to obtain a list of all possible options, you can manually add the entry
RecordDefaults = 1to the [M/Profiles] section of the configuration file. This will cause all values which are used to be written to the configuration file.