Excuse my ignorance but what is Iprefs and what does it do???
It reads your preferences from the saved files and applies them to the system. For example if you run Prefs/Screenmode and click on Save, a file envarc:sys/screenmode.prefs with your settings is created. IPrefs reads this file and changes the screen mode accordingly. Additionally IPrefs keeps watching this file in the background and changes the screen mode whenever new settings are saved to it. The same happens to all the other Prefs programs and prefs files.
So install Cybergraphx drivers after installing 3.9 & Boing Bags 1&2?
If you made the emergency disk after installing Cgx, then Cgx should be contained on the disk and you shouldn't need to install it again.
Did you try to delete the prefs files ? Shouldn't be too difficult and should fix your problem.