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You can find your preference files in the TFDIR_PREFS folder.
The structural preferences are stored in a binary resource file, stfprefs.rsc. When the software is not running, you can try backing up this file by renaming it to something like stfprefs_rsc.001. If you do this and restart the product, you will start with the default "out-of-the-box" preferences. See if that makes a difference.
If that doesn't work, there are a couple of other preference files such as structural.upf (or whatever user name you're using) and tfprefs.rsc in the same folder and you can try the same thing with those.