When I make a change in Preferences, my open documents are not affected.
Preferences are generally for new documents. To change open documents, use the menu bar items.
Bean crashes at startup.
Try dragging the following file to the trash (the file contains Bean’s preference settings) and then restart Bean:
Repeated crashes on startup may be caused by Bean trying to open an autosaved document that contains a problem. Try removing any autosaved documents from the folder:
Try downloading a fresh copy of Bean from www.bean-osx.com.
List Bullets appear out of nowhere.
Erasing the initial bullet isn’t enough to get rid of a list; you have to remove the underlying list attribute. You can do this by applying Format > List > Marker... > None to a text selection, or by applying Edit > Remove > Text Lists to a selection.
Parts of the document disappear in Layout mode.
Probably pagination is being thrown off by invisible text tables copied and pasted from a web browser. Try selecting Edit > Remove > All Text Tables. To reveal hidden text tables, select View > Show Invisibles.
A document file won’t open in Bean.
Bean usually determines a document file's format by looking at the filename's extension (.doc, .rtf and so on). If the filename extension is missing from the filename, try adding it.
How do you make Footnotes, Sections, and automatic Table of Contents?
Bean does not have these features. Try LibreOffice (available at no charge).
Can I write my graduate thesis with Bean?
For some things you just need a full-featured word processor, or else TeX.