This is a note to help prevent others experiencing the same hassle as I did. If you have the Secondary Lightbox enabled and you deactivate and then reactivate the Lightbox Plus plugin (e.g. to test plugin clashes), then the "Use Secondary Lightbox" setting in "Lightbox Plus: Secondary Lightbox Settings" will become unchecked and your Secondary Lightbox settings lost on reactivation. You will need to recheck the box and then re-enter your settings.
Behaviour observed with Lightbox Plus 2.4.6.