We don't have these problems. We use the default settings and in development configure uSync to import Everything at startup with no disabled handlers. In test/live we import Settings at startup with the content handler disabled.
This means default + "export on save" which may not be default.
Make sure you don't do any clean exports, and that you add alll uSync files to source control.
The "still report that there are things to import" happens every now and then but it's always been a false flag... can't give a good example right now.
For Settings I don't believe we've had any problems whatsoever, but for Content we would get the false flags, or even failures if entire root nodes are replaced etc.