MiniDV Audio Sync Issues

[Selur]

The first thing I would recommend, is to try whether enabling "Config->Input->Decoding->CFR output" helps.
Also mediaifno reports:

Delay                                    : 634
Delay                                    : 634 ms
Delay                                    : 634 ms
Delay                                    : 634 ms
Delay                                    : 00:00:00.634
Delay                                    : 00:00:00.634
Delay, origin                            : Stream
Delay, origin                            : Raw stream
Delay relative to video                  : 0
Delay relative to video                  : 00:00:00.000
Delay relative to video                  : 00:00:00.000

since the delay relative to video is zero, there should be no delay.
And the only delay that gets added for the muxing is to compensate the encoder delay.
Which 41ms in your case.
This looks all fine.

To check that the intermediate files are okay, you could enabled "Containers->General->Keep intermediate files" and check the length of the extracted and reencoded files.

The audio and video reencoding calls seems correct and I can see no 'warnings' or similar in the log that would directly idicate a problem.

Does the delay stay constant form the beginning to the end or does it seem to change?

Cu Selur