We're attempting to upgrade a site from 4.9.5 -> 5.6.1 and the installation process went succesfully with no issues.  However afterwards going to the Host Settings page results in a permissions issue in relation to jQuery.  We moved the app from Medium trust to Full trust and the page loads but now the system shows the jQuery version as "jQuery is not installed."  We checked the system path and all of the files are in place for it in the correct location.  It made no sense why we would get an IO permissions issue for jQuery so I loaded up FileMon and watched for requests for jQuery.  Well loading the Host Settings page triggered two calls, one for jquery.js and another for jquery.min.js but the location was the issue.

D:\temp\Shared\Scripts\jquery

We don't even have a d:\temp folder on the server yet it's still trying to locate the files in that location.  We're running DNN with some modifications to the skins but we have not modified the source of DNN at all though.

We've now upgraded to 6.0.2 and we continue to have this odd behavior of it trying to access the jQuery files from paths outside of the website.  However now placing all of the fles in the location it's looking at is no longer solving the problem.