I've got Logos Bible Software 4.5c SR-3 (4.53.0.2294) installed on OS X 10.8 (Mountain Lion) - which may be the cause of the problem... hadn't been able to test it in Lion yet.
I opened an existing Note file, went to an existing note entry, selected an existing bullet point (where I had left off), click the button to move the indentation of the bullet point to the right and Logos exits.
Known issue? Need logs? What's next?