Scheduled Jobs not running after site upgrade

After an upgrade of a customer site from EPiServer 5 to EPiServer 6 all scheduled jobs stopped working in all environments. When debugging the scheduling service (in a command prompt run "EPiServer.SchedulerSvc.exe DEBUG" in the service directory) we noticed that when the service tried to connect to the site it failed with the following error message,

#INF# [_LM_W3SVC_1_ROOT] Failed calling site (Attempting to deserialize an empty stream.)

We tried to clear the "EPiServer.SchedulerService.Sites.xml" file to force a re-registration of the site but it never registered. After some thinking and contact with EPiServer support we found the fault, a missing module in Web.config. When we added the "FirstBeginRequestModule" module to the modules section everything started working again.

<configuration>
  <system.webServer>
    <modules runAllManagedModulesForAllRequests="true">
      <add name="FirstBeginRequestModule" precondition="managedHandler" type="EPiServer.Web.InitializationModule, EPiServer">
    </modules>
  </system.webServer>
</configuration>