Preferences keep going missing

This is really strange. On my Mac Pro (quad core) running 10.5.1, I keep having preferences go missing. This didn't start happening until after I'd upgraded to Leopard and started using Time Machine for backups, but I can't pinpoint the cause.
I had been using a notepad program called Sidenote which stores notes in ~/Library/Application Support/Sidenote. One day, all the notes were gone and I had to restore them using Time Machine.
I use a utility called Textpander that does autotyping. Several times now I've tried to activate it to find all my preferences gone. Those are stored in ~/Library/Application Support/Textpander. I had to restore the settings with Time Machine each time.
Twice now, after plugging in my iPhone and going to iTunes, I've found that the checkboxes in the Info tab to sync the Address Book, Calendar and Safari bookmarks have been unchecked. I have no idea where those settings are kept. Luckily, the settings in all the other tabs seem unaffected.
I have to wonder what other of my preferences are going missing and I haven't noticed yet. Nobody else uses my Mac. I don't run much "weird" software. My Mac never sleeps; it stays on all day and all night unless I have to restart it for some reason or I'm going away for the weekend.
What could possibly cause this?

There is a display bug, but it still works okay -
I prefer Arial to the default Helvetica, so that's what I set -
When I first open a new message window, it displays Helvetica as the font -
However, as soon as I type the first character, it switches to showing Arial as the font -
...and actually enters in Arial.

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