I ran into the same problem--I was able to fix it on my end, but I'm not exactly sure why it fixed it. I'll explain what I did--you might look into it as well.
When I originally federated my Portal, I didn't have a web adaptor configured with ArcGIS Server. So when federating, I used port 6443 for both the Services URL and the Administration URL. Setup this way, I watched Fiddler while running an analysis task in Portal. Looking at the input parameters for the SubmitJob task in Fiddler, all of the services are being called and created over ports 6443 and 6080. I don't know that this is inherently wrong or not, it just struck me as abnormal.
I installed a web adaptor for ArcGIS Server (separate from the Portal web adaptor, which is required), and un-federated and re-federated, using the web adaptor URL for the Services URL. After doing this, Analysis worked successfully.