Hi – I’m sorry to see you are hitting problems here.
Thanks also for testing with all other plugins deactivated: can I ask you to repeat that test, but also switch to a default, unmodified theme (such as Twenty Twelve / Twenty Thirteen) – does the problem still occur under those conditions?
Not knowing how your theme has been put together it is really difficult to answer that. My guess is that somewhere in their code they have a filter set up on the_content that is overwriting things for some reason. Would it be possible for you to touch base with the theme author and ask them if indeed they are doing that?