Maybe this can help you:
If TMPGEnc says that the video time / runtime is way too long
TMPGEnc keeps encoding after the end of video with only a black screen
Try change the directshow reader priority, in TMPGEnc under Option->Environmental settings->VFAPI plug-in and right click on the DirectShow Multimedia File Reader and increase the priority to 2 or to the top of the plugin-list and reopen the video.
If that doesn\'t help try convert the audio to WAV audio before converting and use the wav as audio source.
And if all that didn\'t help you can always use the source range to select exact what to encode, under Settings->Advanced in TMPGEnc.