VLC doesn't use Haali. In fact I am allmost sure it's using Gabest.
I don't use Haali so I am not sure if my memory of it's configuration it's good.
On the other hand, I see your Haali is from 2009. On it's developper site it writes:
14/08/2010
- Fixed items:
- Fixed aspect ratio processing in certain Matroska files, which caused errors on open
20/05/2010
- New Features:
- Added support for WebM files
- Fixed items:
- Fixed a lot of issues with mp4 muxer
- Better support for VC-1 in MPEG Transport streams
27/03/2010
- New Features:
- Added AC-3 in MP4 support
- Fixed items:
- Show error code in GDSMux when muxing is aborted
- Accept more AAC media types in the muxer
- Use correct timescales when processing MP4 edit lists
- Scan the folder for more segments only if the file references external segments
So, maybe an update can solve the problems.