Good morning Anderton and Keith!
Perhaps my wording happened to be too general, apologies for that. I did a small test on some of the preferences, and they appear to persist, so I would be incorrect to say that no preferences persist whatsoever.
It appears that the biggest issues are the drum maps and clock settings. The reasoning behind drums map I feel is obvious, but as for clock settings, I have that set a certain way so my interface doesn't cause everything on my computer to play slightly faster than they should.
I also suppose I should have been more specific about the visual oddity: essentially what had happened was when I hit play, the clock would jump a few seconds ahead instead of displaying actual time. The marker itself moved ever so slightly, but never to the right spot.
After a few re-openings, that seems to have cleared up, though, fortunately.
Thanks for taking the time to try to assist me! =-)