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When you uncheck the 'Enabled' option under 'File status auto-detection' in the Misc tab of the preferences dialog the setting is only saved until you exit the program. When you start the program again the option is ticked again.
Logged In: NO
"Update silently" and "Scroll to the last line" aren't saved either.
Disabling/enabling directly in config.xml works:
OFF <GUIConfig name="Auto-detection">no</GUIConfig>
AUTO or silently <GUIConfig name="Auto-detection">auto</GUIConfig>
BUT, you must do it with regular notepad or other editor - or your changes will be blown up on exit.
 Scroll to the last... must be new in 5.0 - I don't know how to turn that on.
Could this bug be fixed anytime soon?
Editing the config.xml directly doesn't seem to work.
I think I just found why "Update silently" and "Scroll to the last line after update" keep resetting back to "on" status. I just had to stop the Document Monitor plug-in! Don't know why it was on in the first place.