First of all, could you tell me what version of AME you are using?
Did you import files directly into AME or queue jobs from Premiere Pro or other Adobe apps?
Could you clear the following cache folders while no Adobe app is running and try again?
/Users/<user name>/Library/Application Support/Adobe/Common/Media Cache
/Users/<user name>/Library/Application Support/Adobe/Common/Media Cache Files
How many files did you encode at one time? If you encode one at a time, does it encode fine?