This can happen if the runAllManagedModulesForAllRequests="true" attribute was removed during the upgrade process from the web.config file. Can you please make sure that this property still there?
<system.webServer>
...
<modules runAllManagedModulesForAllRequests="true">
<remove name="WebDAVModule" />
<remove name="XHtmlModule" />
<remove name="CMSApplicationModule" />
...
</modules>
...
</system.webServer>