I think this be related to either of the two following reasons:
- There might be a problem, if you store apps on an SD card. Do you do so?
- Maybe there is a problem with permissions (i.e. the FP updater cant save the position of the apps because it only has read access of the settings file).
Both of the guesses are shots into the wild.
A quick workaround would be to install a different Android Launcher.