Well, the program you suggested
> http://kgiii.info/windows/all/general/startupapps.html
didn't solve the problem, but it did lead me to the solution (it is for this
reason I rate the response as "answered the question", but it could use an
intermediate level). If both lists were reacting as one then the only logical
conclusion is that they are referencing the same folder. This would also
explain why the other folder had no effect.
I did a search in the registry and this is what I came up with:

[HKCU\Software\Microsoft\Windows\CurrentVersion\Exp lorer\Shell Folders]
Startup="C:\Documents and Settings\All Users\Start Menu\Programs\Startup"

where "All Users" should have been my username.

This may have happened when I moved the folder in the first place, which
means Windows made the change without notification and without checking that
it wasn't creating such a double reference.