You got me confused with all that going back and forth between BIC and Fusion!
Anyway, I have an idea of what might be happening: as you are probably aware, WorkShelf and NextSTART, although being individual programs, can also work as a suite. What this means is that they can communicate with each other so that, among other things, when switching themes in one the other automatically assumes the same theme.
This Theme Integration feature can be turned on and off by a switch in
both applications. Open NextSTART and WorkShelf Preferences, navigate to the Themes tab and click on the Theme Options button. A dialog panel with open and in it you will find a 'Enable Theme Integration' check box.
My guess is that you have this option turned on in one of the applications but off in the other (ok, my mistake, I agree that this check box should affect both applications, regardless of which application you used to toggle it).
Either that
or you have the Preferences panel of, say NextSTART, open when you switch themes in WorkShelf (and vice-versa). This has the potential to confuse NextSTART when you close its Preferences panel.