I installed the bitnami ownCloud 9.01 on Debian 8 running LXDE. On the ownCloud setting page, under File Handling -- Maximum Upload Size, the default (according to the GUI) is 513 MB. Underneath that was a message stating "missing permissions to edit from here."
I resolved it with a brute-force changing of permissions on .htaccess and .user.ini, setting R/W permissions for Everyone. I was then able to edit the size in the GUI and have it "stick."
I don't know if the right way to fix this is with a chown or with a more restrictive change to the permissions, but I wanted to give you a heads-up.