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I encountered a similar issue using jQuery Mobile and jPlayer together. When changing between pages in Firefox, audio would cut out and then return after a few seconds. It worked flawlessly in Chrome - audio was seamless - but Firefox was a poor experience.

After some digging, I figured this out: Basically - jPlayer falls back to Flash in Firefox (rather than using HTML5) and adds a Flash element to the DOM. if this element is hidden and re-shown or moved, Flash 'resets' and the SWF file needs to be re-downloaded (I'm assuming for security reasons). When a page change occurs, the Flash element ends up being hidden and re-shown. jPlayer has logic in the code to handle this situation and tries to start from your last position, which is likely why my audio returns and josteinaj's doesn't. 

So, the solution is to make sure your jPlayer is outside both the page element and also the $.mobile.pageContainer element (by default, the parent of the page element). In my case, this was the body tag, which meant the entire page (and thus Flash object) was being shown/hidden between page changes which made Firefox angry. Simply adding an extra div around my page element did the trick.

Hope this helps.