I have only seen this problem after a new build but it does happen regularly. Upon launching AlphaCocoa for the first time, I usually add the LaTeX menu as one that is always on. If I subsequently quit AlphaCocoa without having opened a window in TeX mode then a Menu update proc error is thrown (see attached). It doesn't happen if a window has been open in TeX mode. I presume that it is an initialisation problem: a variable is not set by the loading of the menu, even though the loading of the menu is sufficient to cause AlphaCocoa to look for it on quitting.
I can't reproduce this with the latest code. Maybe this has been fixed by the recent complete revision of TeX mode. Let's see if the bug persists with forthcoming version 9.0a3.
I can no longer reproduce this either. I suggest that this bug be closed. It can always be re-opened if the problem recurs.
The issue seems to have vanished after revision of TeX mode. Closing now.