When looking more closely at this I found that because of the GUI being broken the red Reload Config button had disappeared, however, I discovered a hyperlink at the top of the screen to reload the configuration. Having clicked on this and after completion of the configuration reload a browser refresh brought the GUI back to life.
To confirm I carried out the upgrade on another system that i am preparing for production and exactly the same thing happened. I resolved the problem in the same way.
This gave me confidence to try the module upgrade on a production system, same thing happened and the problem was resolved in the same way.
FreePBX appears to be functioning normally on all systems since then.
Oh, I understand but its the first time I have seen it interfere with the GUI in this way, before the GUI has always come back after the module upgrade with the red button to do the reload, this time it was very odd and quite different!