Could you please send me the web.config files of two of the sites?I have converted the thread to a support one, so you could attach them.
If you only want to have the pages separated for each web site, you should only change this application name:
| applicationName="/App1" //App2, App3, etc
| type="Telerik.Cms.Data.DefaultProvider, Telerik.Cms.Data" />
I suspect that you have also touched the Generic Content's provider applicationName as well.
Following the above instructions, I was able to run 2 applications using the same database, sharing all the content but the pages.
the Telerik team