You could have a trawl through here to see if anything helps click here and click here
On the second link there is this section "If you get No audio or Audio sync problems or any Audio error
Try to convert the audio to WAV audio before converting and use the WAV as audio source. (TMPGEnc can't handle VBR MP3 and AC3 that well). Read the audio to WAV audio guide.", which looks if it may offer you some things to try.