The web.config "httpRuntime executionTimeout" is only for configuring a HTTP request/session.

http://msdn.microsoft.com/en-us/library/system.web.configuration.httpruntimesection.executiontimeout%28v=vs.110%29.aspx

I can see why that would affect manual runs, however the System Report Timeout property should be causing them to fail after 30 mins.

Check that the individual reports do not have a Report Timeout property set to override the default.