I think I found the problem. The guide for setting up OctoPrint doesn't mention telling the virtual environment where Python is installed. Only in migration page here does it tell you to do so. I hadn't so am surprised I had it working at all..
If you don't tell it which python to use it uses the system default. That's only slowly moving to python 3, hence the explicit declaration in the migration guide for plugin devs.
Well, whichever the issue, I don't recall there being a bin/Python directory. I made a total mes of something else so ended up re-creating the SD card image. Wasn't that a joy to go through.... (Sarcasm there) but when I get it all back up and running I'll try another go at migration and see what happens.
Performed, works perfect without any problems!