This occurs for any VaultWiki BB-Codes that collide with vBulletin BB-Codes, when the vBulletin BB-Code is preferred over the VaultWiki BB-Code. Instead of gracefully falling back to the vB version when the VaultWiki code is disabled, both variants end up disabled. Additionally, the fallbacks are hard-coded, which is not foresighted. Instead of falling back to hard-coded vBulletin BB-Codes, we should create save states for each BB-Code before vBulletin overwrites them with found custom BB-Codes.
This is fixed on your site, and also for Alpha 2.