I am sorry if I am stating the obvious, but have you tried a complete uninstall and reinstall of MB?
Where I am going with this is that I had a similar type issue when I installed iTunes, don't even say it, I needed the libraries for encoding. Anyway, after a few times in there, I found that I was no longer able to access the custom settings for AAC encoding. Nothing that could really been explained, why one menu item could not be used, but all others were just fine, as was that setting, at the current as it could not be changed. A full uninstall (all files, config, settings, everything) and reinstall fixed the issue. What exactly happened, don't know, but I guess it was a corrupted settings file. A regular, select normal uninstall, did not fix the issue.
So, maybe you have a similar type issue? You also said you did a upgrade from 2.4 to 2.5, at which time this stopped working. Maybe something got a bit corrupted on the update?