Have you tried setting the Document Properties for your double-sided form file only? File > Properties > Advanced tab and then set the Duplexmode. This will set this propertyfor just this specific PDF.
Did this resolve the issue? I am having the same problem. I am using XI Pro. If this is the fix do I need to make those changes in the individual double sided documents before I add them to the portfolio or after? I cant find the settings after I have added the files to the portfolio.
Right now everything is printing duplex and I can not figure out why because it appears it is set to simplex.