Make sure the css and javascript code is moved outside the editable region or the paths may not be updated properly... most likely this is the issue.
You should, however, leave your css conditional code in an editable region. It will not be updated properly by dreamweaver, so you will have to manually update the paths on the resulting pages in different sub-directories. If all of the pages are in the same directory, you can update the path directly on the template to match the correct final path insted of the template relative path and move it ouside the editable region as well.