Are the user filters set on the published datasource? If so, try removing the filter from the published datasource and embed the filter in the workbook as a datasource filter that is pointed at the datasource. We ran into this issue with user filters on 10.3, and this is the way we got around it. Not the most elegant, but it worked.
Just wanted to update this thread. A Tableau Support case has been submitted and our Engineers are currently working with Patricia to troubleshoot further.