When we migrated the server, we didn't copy over old .ini, .cnf or .conf files because we wanted to make sure the settings files were all valid for the versions we put in. We forgot that MySQL's FullText Search has a default search word length of 4 letters which overrides vBulletin settings (set to 3 letters).
It's still chugging away indexing. I forgot how long this takes. We have a lot of posts so it's a long process. I'm extimatng it's about 50% done about now, so there's still a ways to go.
As an FYI:
FullText Search in vBulletin