I did not assume this was a bug. I usually assume (by experience) that I'm the cause of the problem

I love you for this statement alone lol...
I don't recall reading something about the dependency between UBB and the settings for the full text index in MySQL in the Administrator Guide. I may have overlooked that.
As the UBB is a web script that runs on PHP/MySQL/Apache, it is at the mercy of all three services and how they're configured; if one is "botched" it wont' run properly; though i do think there should be a FAQ somewhere that mentions such things...