Multiple issues

[Selur]

Steps to reproduce:
1.DVD input
2.Select VIDEO_TS folder
3.Audio: "auto add (first) " (in my case AC3)
4.Audio tab: check box "Audio Encoding Option", select PCM
5.Select QTMC de-interlacer
6.Select output: avi/FFvHuff
Run.

Not so good,...
from the tool-top of the 'Processing->Audio'-ComboBox:

...
- auto add (first): enables the Audio-tab, but automatically adds the first input audio stream from the input file to the audi job queue with the settings defined in the Audio-tab.
side notes:
- You can still add additional audio streams in the Audio-tab, unless you use multiple input files.
- This setting will not adjust to changes after loading the source! So configure the Audio-tab before loading your source.
...

So the order of your steps is wrong to archive what you want.

About the length of the audio streams: This might happen since Avisynth/Vapoursynth can't properly process DVDs and thus stumble over DVD titles with an intro at the end/beginning that they skip or not skip, but mplayer does.
-> will look into that later

Real problem is that there is a '01_44_20_3610_02_recalc' job and there shouldn't be one since Huffyuv doesn't use 2pass or bitrate based encoding.
-> will look at it after work
Problem is this is triggered through one specifc order of steps, which I could reproduce once, but not again so far.
Please reset your defaults and try to reproduce this again with a debug output enabled. Problem is that I can't find the exact steps to reproduce this.

Cu Selur