Halc and robertb,
The settings that I have changed on my Win98SE box seem to be sticking, but I am not using a Plextor Premium and so don't have access to the Q-Check tests.
It seems that the unsticky preference problems that you are experiencing are in the Q-Check section. Does the rest of the program retain settings properly? It seems that the program has two parts, the main section and Q-Check which works only with the Plextor Premium. From your reports, this seems to be a bug in which PlexTools hasn't extended the save settings option to the Q-Check section. If you have reported it to Plextor, they should fix it in a later release.