I think in the case of acad it only saves values that are different than the default. I looked at the code and this was apparently done because you’d get an extra set of defaults for each language you had installed and this somehow fixed that (not my code, looks like that change occurred in September of 2008). With regard to settings alone, the acad plugin has changed minimally since V5, the code under the hood for saving and retrieving settings is all different now though.
Iges saves the whole set of options (altered or not) after the UI is complete. Probably less efficient but I haven’t heard anyone complaining about that yet.
Is WorkNC one of our plugins? I’m not familiar with that one. Is it a V6 plugin? If it is it’s supposed to write that stuff to %appdata%, not the registry. If it’s V5 it may still save that stuff to registry.