In the version 1.5, I have added an option not to use AJAX Libraries from Google for Joomla Administrator.
I must say that I spend hours changing all configuration setting that could impact on that to no avail. I deeply frustrated with the product and if I don't find a solution urgently I will give it up.
I think that the problem in your case will be most likely neither in configuration or JoomSEF, but in incorectly created links within your site.
JoomSEF will translate the links it detects. If you have wrong link created within site, it will result in wrong (or duplicate) SEF URL.