I've found with the recent versions of FFP, auto-update causes some of the local FF references--namely, the Start menu Internet link and Add/Remove programs entry--to point to FFP.
The first time this happened I was very confused, as after I removed my JumpDrive and attempted to launch my local copy of FF from the top of the Start menu, Windows gave me an error. I've since figured out the problem, and it seems the only solution is to update FFP *first*, then update the local copy. Either that or reinstall local FF after updating FFP.
Not sure if the bug is on Mozilla's end or John's, but this is, IMO, a show-stopping bug, and when I looked through the forum beforehand I couldn't find any references to this problem. So I figured I'd post about it.
Off-topic: Don't count on me being back for good. I'll probably leave just as quickly as I came (Yes. Again! :p).