I used to run a Bitnami installation (until a couple of months ago), From what I know, the web server is supposed to run as user ādaemonā (which belongs to group ābitnamiā).
So your cron seems to be running as the correct user, but for some reason the web server isnāt (if Iām not mistaken).
If you can try changing your web server to run as daemon/bitnami, then fix all permissions manually for one last time, then things should run smoothly in the future.
My only suggestion is to look for Bitnami-specific instructions, theyāre quite peculiar. My experience asking for help in their forums is very positive.
I solved the problem. After looking at problem directories during the upgrade, I realized that they all were using daemon user/group, so I changed my crontab to run under the user ādaemonā. That solved the problem.