The problem I've had is probably related to this... I'm on Orange in the UK by the way.
I've found that "Listen" - the podcast application - doesn't like handing back control of the inline controls when I stop using it and go back to using the stock music player. In fact I've just had a another play with it and it now seems impossible to get the inline controls do anything except interact with Listen. Maybe a hard reset would clear the way the controls seem to be permanently attached to just one application, but I'm not inclined to try that.
I don't know quite how Android is supposed to know which application is in charge of things, but it seems to be a first come first served idea taken to a ridiculous extreme!