Found the issue. It was my Unreal Weather mod, in the community folder. It seems to stop the loading, and MSFS just waits till whatever it is finished doing. I have now removed it permanently and will stick with the slightly unreliable LIVE weather :P. Not sure why it was impacting the log in response (black square on screen while logging into MS Live) and the very long “checking for updates” (upwards of 5 minutes). But is seems to have resolved both these issues and the long loading following these screens.