The auto-content setting for the filter field is not saved either when I save the lister as a layout or when I set it as the default lister ... It remains turned off when I attempt to restart either the default or load the saved layout.
That setting isn't saved as part of the Layout, it belongs to the actual filter field itself. To change the defaults you need to edit the button and set the Args field appropriately.
The HELP says " The keyword to set this option on by default is auto content".
and beneath that says the following:
You can specify the default filter modes by editing the field and specifying the following keywords in the Args field of the button editor:
· files – show only matching files (the default is both files and folders)
· folders – show only matching folders
· hide – hide matching items rather than showing them
· realtime – filter in real-time
· nopartial – no partial matching
· local – enable View Filter mode
I tried entering "auto content" as the keyword/argument .... It had no affect and is not listed above as an availabel argument although the help line I qutoed seems to indicate it.
At any rate, I entered "auto content" as an argument and it had no affect.
Nevermind ... the help forgot the concept KEYWORD and not keywordS 
I put in AUTOCONTENT as one word and it worked fine .
Oops, looks like a small error in the docs there 
Glad you got it working!
Looks like you've solved it and I'm too late, but just in case this post about the filter boxes might be useful to you or anyone else who finds this topic:
[resource.dopus.com/t/legacy-faq-add-and-configure-filter-boxes/1314/1)