Right I'm not saying it's a solution, but it narrows down the problem.
If shortcode works, that means the problem is happening in the "the_content" WordPress filter. If the fix theme option solves the problem, that that indicates the problem is with "the_content" filter in JetPack being called before the page is loaded. If the define I gave you fixes the problem, that means the problem is caused by how JetPack is handling "the_content" filter after PowerPress adds it's content to the page. If none of these things point to the problem, then I'm going to have a long weekend trying to figure out what's happening. Once I know which is the problem, I can include a temporary fix in PowerPress, similar to the one I added for when the Facebook app had this problem.