I have been banging my head against an issue where I could use 9.1.0 with HTTP but not HTTPS with my new Let's Encrypt cert. After some testing it seemed like mod_rewrite wasn't working and I was getting a 404 error any time I tried to use SSL.
I finally gave up and was getting configs together to do a bug report and noticed the Include LE injects in my SSL virtual included:
tucked in with the other settings - it prevents URL path stuff after the /index.php so things like /index.php/login returns a 404. Ouch!
Fixed now, but my I thought I shoud share in case others had similar symptoms.