With some input video (such as LQ MP4 from [1]), the second pass fails when a preset enabling automatic placement of alternate reference frames with ”auto-alt-ref=1” (such as all of those provided by libav-tools) is used. (Example of non-problematic input is MP4 from [2].) This is apparently an upstream issue, already fixed in v1.1.0-184-g429743c [3].

Steps to reproduce:
1. wget ’http://archive.org/download/Mario2_919/Mario2_919_LQ.avi’
2. avconv -y -i Mario2_919_LQ.avi -c:v libvpx -pre libvpx-360p -pass 1 -an -sn -t 1 out.webm
3. avconv -y -i Mario2_919_LQ.avi -c:v libvpx -pre libvpx-360p -pass 2 -an -sn -t 1 out.webm

What happens:
The second pass ends with:
[webm @ 0x7ab6c0] Application provided invalid, non monotonically increasing dts to muxer in stream 0: 100 >= 100
av_interleaved_write_frame(): Invalid argument

What I expect to happen:
The second pass to finish successfully.

Workaround:
Copy preset file to ˝/.avconv/, comment out (#) auto-alt-ref=1.

*[1] http://archive.org/details/Mario2_919
*[2] http://archive.org/details/014674
*[3] http://code.google.com/p/webm/issues/detail?id=468#issueheader