Limited Access Issue Continued

In a previous post, I talked about a user that had limited access to a folder within a document library, but no access to the library, nor the site, and the user was not able to access the folder despite being given access.  Microsoft helped me solve that issue by disabling viewformpageslockdown.

However, the issue persisted on a couple of sites within the site collection, even though the site collection at large was fixed.  The only commonality with the sites that were still having problems was that I had used Metalogix Migration tool to copy the entire site over to the new environment from SharePoint 2007 to 2010.  Most of the other sites, I used the tool to copy data (i.e. lists and libraries), but not the entire site.  I had setup the site on the new environment and copied information into it.


After a lot of frustrating poking around, I noticed this within permission levels for the site:

 

If you go to Site Permissions for the particular site, there is a Permission Levels button that takes you to permission levels for the individual site.  I clicked Inherit Permission Levels and it fixed the problem for that site.  After clicking that, the Permission Levels button disappeared for that site, now I can only access permission levels from the root site.