Have you tried the Adobe forums? I would think this would be a much discussed issue if it's prevalent.
I don't have a solution but we gave up on Adobe Media Encoder back at version CS3. It's always been extremely buggy and inconsistent and frankly just not at a level where we could trust it in a professional environment. Products from Telestream, Grass Valley (Procoder), and Sorensen are much more robust and reliable and are well worth their modest cost.