Curiously, there is sparse information on this subject on the Web and none (at least, that I can find) in the jQuery Mobile documentation or the four books I have specifically on jQuery Mobile. Curious, because it is a very important question where good search engine page ranking is concerned.
After the first page is loaded, jQuery Mobile will grab the unique title from the head section of any subsequent page, when that page is a separate URL entity. However, everything else in that head section is ignored. You can programmatically change the meta description in the DOM, but I don't think a Search Engine bot is going to see it at that point.
This is an important concern, as that description is what search engines show to attract people to your site. I have spent hours searching for reliable information. A couple of people have mentioned that the problem is non-existent because the search engine bot is going to read all the text on the page and recognize the header information on that particular page. I am not so certain that is correct, as I believe (correct me if I am wrong) the bot is going to see what the page displays and what the page is going to display is the head section of the first file opened on the site - NOT that of the current file.
This is pretty important to me. I have a client loosing faith in me because his SEO people don't understand JQM at all and are at odds with me on this mobile version of the site.