I just ran into the same issue. Looks like a bug...
Please open a case.
I had this issue early this week and was stumped.... we eventually figured it out.
The problem happened when we did a lot of development to a workbook demoed it locally and then published to the server. All along never closing the workbook.
The fix was to publish it to the server, close out of all tableau instances that were local on my machine. Then download the workbook and reapply the Apply filter button, when I re-downloaded it from tableau server it was unchecked. Then publish and it worked.
There is a knowledge article somewhere on this site about this work around as well.
Thanks for the solution!