macdude, I’ve never noticed a similar problem using 1.4.3 - or earlier versions - on OS X. And I’ve never had to go through all of the steps you’ve listed as a fix.
The only way - if Scribus is working correctly - that a style should be “nested” is if the “Based On” field is filled. If the style isn’t based on anything the style should be listed as a “root” style, i.e. directly under the Default Paragraph Style without indentation.
Would it be possible for you to provide a document that exhibits the issue so it can be examined?