I do not use a Macintosh, but if I were experiencing this problem on my (Linux) machine, the first thing I would try would be to delete (or move to a backup) the .TeXmacs directory in my home directory. This is the directory that saves many of your settings, and it is possible that something there has become corrupted. If you delete this, and then run TeXmacs again, the directory will be recreated from scratch -- hopefully without any of the issues you currently see.
I'm not sure where this directory is on OS X, but perhaps you may know it, or you may get a reply from someone with more experience with Apples.
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