Why do I get broken WAV files with shorter duration after conversion?

Short answer: Because of the 4 GB file size limit of the WAV format. The size of the file is declared by 4 bytes only in the WAV file header.
This is a common problem when converting multi-track audio from a Blu-Ray or DVD for editing. Many players and other software like Premiere Pro cannot read the files correctly.

Possible solution: Take your source file (in my case a 6-track DTS-HD master audio stream), open it with the free software Audacity and export the file in chunks that are under 4 GB. Really simple actually.

Now Premiere Pro does not recognize more than one track (no surround, says the track is mono)? Just use SoX with the arguments "sox input.wav output.wav" and it will fix the channels so they get recognized correctly.