I can only reproduce this behavior if:
1. I disable VaultWiki.
2. I re-enable VaultWiki.
3. Before the enable-rebuild is done, I visit a wiki page. The wiki page has no BB-Codes parsed.
However, once:
4. The enable-rebuild completes,
If I refresh the browser on the affected page, the BB-Code is now parsed. The behavior may persist for guests viewing XF2's guest-cache until the guest-cache for the page expires.
Before Beta 1, the BB-Code remained unparsed, but Beta 1 has new code that detects this situation. In my tests, the new code appears to be working as expected (including after upgrading). If you are experiencing something different, then please submit a ticket while the issue is still occurring so that we can investigate on your test board.
Since XenForo 2 rebuilds the BB-Code cache while the class-extension cache still doesn't have VaultWiki extensions active, there will always be a period between the stock rebuild and the next request when VaultWiki can force the BB-Code cache to be rebuilt again. Short of XenForo 2 redesigning the active-state rebuilds so that code-event listeners and class-extensions are first, with all other rebuilds in a subsequent request, this issue will persist.