I've upgraded a site to 4.0.0.0 MSSQL and the site is working fine, but on attempting /setup/default.aspx the usual upgrade page includes this:

Error Occurred

The Data folder beneath the root of the web site is not writable by the website application pool identity. You need to make this folder and all its child folders and files writable before setup can proceed. mojoPortal needs this to be able to write search index files, error logs, image gallery uploads, and other important features. Right Click the Data folder in Windows File Explorer, choose properties and go to the Security tab. Depending on your setup, you will need to either grant write permission to the "IUSRS" group or to the "IIS AppPool\" user. Obviously, instructions will be different across hosting environments but the same principle is true, the Data folder and all its child objects must be writable.

But I also see, further down, 

Setup Complete

Setup has finished successfully

I think this permissions message is erroneous, as I can upload files using the File Manager, which is writing into the Data folder as the application pool identity. But I'm concerned whether this message means something has not upgraded fully.

Can you advise?