Turns out this is a problem with -pre vs -preset in avconv. All this ffmpeg fork avconv broke the community for everyone but the developers. Now a Google search for useful information on any tool is useless.
For those who get here on a similar issue, I translated mp4 to webm.
avconv -i "$inputFile" -threads 8 -s 1280x720 -preset libvpx-720p -b 3900k -pass 1 -an -f webm -y "$outputFile" avconv -i "$inputFile" -threads 8 -preset libvpx-720p -pass 2 -b 3900k -acodec libvorbis -ar 44100 -ac 2 -ab 128k -f webm -y "$outputFile"
This is for 720P mp4 to 720P WEBM. You can easily configure 1080P, preset exists.
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