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I've made some changes on my local machine to my app to how a matplotlib graphics is displayed. I'm happy the results, checked in the changes to GitHub then did a git pull to a directory on PA and restarted the server. Different results.
I switched directories to a place where an exact version of the same app is running on PA did the git pull, server restart and viola' the changes appear. Is there some PA magic that I don't understand at play here?

I'm having trouble following what's the same and what's different to what. It sounds like you have a different environment at some point. Check the things that are not as you expect and compare their environment (Python version, packges installed, virtualenv etc.) with the ones that are as you expect.