Audio-Video out of sync after merging encoded DV or VOB clips?

There is a fundamental problem when merging AVI-files with MP3 sound, that
have been transcoded individually. As far as I know, it needs a certain
amount of raw PCM data to make a single MP3 encoded frame. At the end of the
encoding process, this condition is almost never fulfilled. Therefore,
some audio data are simply not encoded, or, using option -O,
PCM data (silence) are padded to make a final MP3 frame. In the former case,
sound is too short in time, whereas in the latter, the audio played
by a player exceeds the video playtime. This may be only a couple
milliseconds but adds up when merging the clips.

Why does it work for transcode using option "-t" or DVD chapter mode "-U" ?

In this case, the MP3 encoder is never switched off. Buffered audio data
never get lost. After merging, audio and video are OK (in theory).
This is also the reason, why the cluster mode must use this approach encoding
the audio in a separate step, unless you want to use raw PCM audio data.

Now what to do with tons of DV AVI-file clips, you want to merge, but
only after encoding?

The "directory mode" with option "-i" also works for DV AVI-files (hopefully).
Try to put all clips into a directory and use the directory name
to let transcode extract and merge the raw DV stream for further processing.