You have to turn on both "Enable advanced graph building", and "Allow intermediate filters." And you likely want to disable subtitles in BSP too, but do not disable VobSubs. If the file actually has a VobSub track and BSP is VobSubs are turned off it will crash, you just are forced to have two sets of subtitles for now.
If you aren't using the latest BSP you could possibly be correct that it is not loading for you. Many versions directly after build 820 were completely broken for VSFilter and Haali support. The latest will work with VSFilter correctly except for vobsubs.
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