Is your pano head adjusted correctly? I think it would be hard to adjust one using a Leica as it would take a lot of trial and error. That is one reason why the M8 needs live view! I use a Nodal Ninja head and they provide the information for setting it with various lenses and bodies. This makes it very easy to get right.
I shoot and stitch 360 degree virtual tours with perfect results using a pano head, a Canon 15mm fisheye and Autopano. I convert the raw images in DXO but do not correct for the fisheye distortion - Autopano handles it. I don't have to set anything about the focal length in Autopano Pro. Are you using smartblend? Experiment with different amounts of overlap. You may need fewer shots than you think.
Here are some examples - these very wide shots are not always great images but they often help tell the story of a space.
I believe that my pano head is adjusted correctly, although I am not certain. When I got it, I placed the M8 and 16-18-21 on the head, on a table, and took two photos side by side with perhaps 30% overlap. I found two features which were directly above each other in the one photo, and then adjusted the rail until they were above each other in the other photo too. Everything from 30cm to 3m was then correct.
Is a different rail setting necessary for different focusing distances?
However, I noticed later that I had a minor flaw in another panorama, up close, and then I had trouble with the mentioned panoramas. I think I might go back and test the pano rail setting again. I had only set it to 1mm accuracy, but perhaps I need to be more accurate than that.
The other possibility is that I am not overlapping enough. The 16mm is a 21mm on the M8, and I use it in portrait mode, shooting horizontal panoramas. I was turning the ballhead in 45 degree steps, but perhaps I need to back off a little there. I will try 40 degrees the next time.
Another possibility is that there just aren't a lot of unique features on a train platform. Repeating patterns are the rule here. The ceiling also has repeating patterns, so in some places, I could understand it is APP was unable to find unique features and got confused about the positions. Increasing the overlap here might help again.
I will try these changes, hopefully tomorrow. I will let you know how it goes. Thanks for your help.
By the way, setting up the lens in APP before stitching helped a lot, but not completely.