Did you look at the file permissions on the RealTemp.ini file? Other users have reported problems when moving the RealTemp folder and this file from one volume to a different volume.
Both TJMax and the calibration factors get saved correctly and also get reloaded correctly for me so I'm not sure what's going on. Make sure the RealTemp.ini file is not open in another program like Notepad or Wordpad while you are saving your settings or while RealTemp is starting up. I'll have a look at my code to see if I can see any problems that might happen with Atom CPUs.
In the Settings Windows you have to click on OK for your new settings to be saved.