Debian Multimedia :: Avconv Gives Audio And Video Out Of Sync

I have a problem with avconv. Most of the use cases work spledidly, but when I need to crop a segment and then splice multiple segments together, I get problems.

The process I use is this:

1. Raw recording of short segments in high-quality AVI, These are produced by avconv, some as screencast and some by combining a PNG file with flac audio from audacity.

2. Conversion segment by segment into mp4 and ogv
Options A: -acodec aac -strict experimental -ab 128k -ac 2 -vcodec libx264 -s 640x480 -pix_fmt yuv420p -movflags +faststart -crf 22
Options B: -acodec libvorbis -ab 128k -ac 2 -vcodec libtheora -s 640x480 -b 500k

3. Splicing of the segments using MP4Box or oggCat.
(I used to do this in ffmpeg, but I have not figured out how to do it in avconv.)
This works.

In some cases I need to crop the segments, using the copy codecs and the -ss and/or =t options.

If I crop the AVI segments (between 1 and 2) the sound is clipping (this also generates a spree of error messages `Non-monotonous DTS'). If I crop mp4/ogv segments, (between 2 and 3) the remaining video, after the cropped segment are out of sync. I get the same problems with both OGV and MP4 playing them in vlc. Playing the mp4 directly in iceweasel works as it should.