Hi,
Prior to installing MJ I had a separate template for my audio player.
I installed MJ and now the template doesn't switch for my audio player.
I am not sure if the 2 are related as I was doing many things to my website at the time...
So I disabled all the Mobile Joomla plugins, templates and component.
Question that would help me lots would be:
If I disabled MJ does that mean that there is nothing that was permanently changed in Joomla that could explain the issue with the template switching?
Does MJ make permanent changes to Joomla Core files for example?
Or do I need to Uninstall MJ completely so that it no longer effects the website?
Thanks for your help,
Kyle

It's sufficient to unpublish MobileJoomla system plugin to disable MJ functioning.
And MJ doesn't change Joomla core files.

Thank you for letting me know. 
I have literally just a few minutes found a workaround to my solution.
I have had another site which has the same issue that the Templates simply are not switching for a particular page for some reason. This other website never had MJ installed so I now know it's not MJ causing the issue...
I did use Chameleon plugin though to solve the issue and my templates now switch. 
Thanks for your response Dryabov