OK found the issue.
When runnin zap-full-scan.py if you look at the code there are 2 sections - 1 before the spider and 1 before the active scan -
it changes the target to the original host or domain without the trailing directories. it strips the "/" if there are more than 2 (which are the original of the https://)
It's strange since this behaviour is different when i'm running in the UI.