Fixed in the next release. VaultWiki's Syntax option cache wasn't being rebuilt under XenForo when you made changes to it.
Additionally, if any cache was not loaded into memory before trying to rebuild it, it would simply keep the previous version of the cache. This is also fixed in the next release.
Additionally, any BB-Codes with the 'plainChildren' parameter (I remember going on a rant months ago and detailing why Waindigo Tables don't actually need to use it, but they still do) received extra line breaks on VaultWiki pages. They received even more line breaks if the BB-Code was templated. This is also fixed in the next release.