Not sure of the in and outs of what code should be on the page.
You create a template in DW
You then convert this to a Theme.
You add the plugins to the pages created from the theme.
Any changes you make are then made to the DW template not to the theme page.
Is this the process you are using? Its working fine on mine. Probably get more help on Monday when WA guys are back.
Sorry I cant help much more than the process what I use.