The provided code snippet did not help much in solving your issue.
Would you isolate the problem in a sample project and send it to us so we can take a look at it?
There should be a reason in your code responsible for these classes appearance and after that their removal.
I reviewed the sample from here
but I did not find any jquery.mobile-1.3.1.min.css in it. Are you sure this plugin is designed to be compatible with it?
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