There's a toggle that was added back around the time of the unity port (as a result of your request that LeftCtrl and RightCtrl be considered interchangeable, iirc) named "Separate Left And Right Mod Keys", on the interface tab of the settings window. If that's checked, it treats LeftCtrl and RightCtrl as non-interchangeable.
Testing with a riot selected, with and without that toggle (the default is unchecked) :
Toggle Unchecked, LeftCtrl+M pressed => opens ship design menu
Toggle Unchecked, RightCtrl+M pressed => opens ship design menu
Toggle Checked, LeftCtrl+M pressed => opens ship design menu
Toggle Checked, RightCtrl+M pressed => centers on a metal deposit
Is that not what you get?
As for settings not being retained, I suppose it's possible there was some kind of serialization bug messing with those, but I haven't heard other reports that would indicate one.