I'm experiencing the same problem with my Sites since running the 5.6.0 Upgrade. I Posted this in another Thread, maybe it will help some of you temporarily.

There is definately a problem with the 5.6.0 Upgrade. I attempted to Upgrade a number of my 5.5.1 Sites that are Hosted on a Dedicated Server at PowerDNN and I had problems with every one of them.

I had the same problem with the Site not loading correctly unless you clicked on the "Return to Site" botton which essentially adds the Default.aspx ending to the URL.

I figured out the by switching the Sites from ASP.NET 4.0 back to ASP.NET 2.0 under IIS and then removing this text (requestValidationMode="2.0") from one line in the Web.Config (I get a New Error Message if I dont' remove that text) I could get my Site to load normally. The only problem is that now I've got Modules that require ASP.NET 4.0 that are loaded on a few of the Sites that will not work correctly. Someone needs to fix this problem ASAP.

P.S. If I switch the Sites back to ASP.NET 4.0 they become broken again. I played around with this for a couple hours to nail down exactly what was causing this problem.