Glad its working.

fyi the /Setup/Default.aspx page does not do anything with file system permissions, it is not capable of changing them at all. When files are uploaded from one machine to another though the permissions can be lost sometimes because each file has an "owner" sid and the owner sid from one machine is not recognized on another machine.

never fear to run the setup page though, it can never hurt anything

you could remove it or rename it but then you would have to remember to restore it during upgrades.

The best thing is to put this in user.config

<add key="DisableSetup" value="true" />

then it will not execute unless logged in as admin

but every time it executes it can never do any damage.

all it does is loop through each feature looking for any upgrade scripts that are of a higher version than the last one it knows about from the mp_SchemaVersion table and if it finds any it will execute them in version order and store the latest version number in the table mentioned.

Other than that it processes the feature definition files which define the feature settings and their default values. And if no sites exist it would create the first site as well as the admin user and some default content pages which come from config files.

if a site exists and no newer upgrade scripts exist and feature settings have not changed the result is nothing is changed at all