Be careful what you delete. The aircraft-data "flightgear.org/aircraft-data/c172p.xml" file is really the only file that would have any effect on saved settings and that is changed on every launch and eXit, so I don't think that is an issue. If your starting from the QT launcher there is command line settings that can be added to set properties. You didn't add any radio settings there?
You could try opening the sim, set the radios, close the sim the correct way using the "File/Exit" menu choice and the open the saved data file "flightgear.org/aircraft-data/c172p.xml" in a text editor and see if it saves the frequencies correctly.
The "save1.xml" file is created if you use the "Save/Resume" feature. It does not specifically save the radio properties, but probably should be made to.
It shouldn't matter though because they are saved every time anyway.
I was able to verified that the default c172p that is in fgdata does indeed save the radio settings by default. So I really have no clue as to why yours won't.