I am using the installer version, and ConfigDir.ini file was the default one (all lines commented out).
Other options are getting saved, yes.
It seems to me that the options and aliases are getting saved in the %mydocuments%\DonationsCoder\FindAndRunRobot folder, but the plugins are saved in the c:\program files.. folder
If I grant myself (the regular user on the pc) access on the plugins folder then plugin management works, but that is not really a solution.
I would think that the plugins should get saved to the mydocuments folder as well.