I have a mildly similar problem. Anytime I pause the player, it's like it's rewinding the amount of time I have it paused. Was listening to the Bombcast last week, paused it at, let's say, the 30 minute mark. Came back 5 minutes later, and it was a part I had already heard .The timer is still going forward, but the audio is definitely wrong. Been doing this for about a month or 2 for me.
I have this same problem. The progress bar shows me at the end of the file, but I'm definitely not there as the podcast is still playing. I also have the rewinding going on anytime I pause the file and then come back later. I have to listen to ten or twenty minutes of stuff I've already heard, sometimes more.