I would suggest, if you haven't already, raising it with Tableau Support.
The detail you provided is really helpful to them.
Please post back as you progress the issue, as others may join/ find this thread.
I opened a support case. Will update the progress here.
FYI If i remove the data source filter the workbooks generate the (unfiltered) views.
Update: Supplied Logs and some more information to the support
This issue was somehow linked to our Tableau Server.
In the meantime we moved our Tableau Server to another VM-Ware Host and assigned more resources. By now it looks like this has solved the problem.