This will occur if VaultWiki was installed before your BB-Code add-on, so VaultWiki's table BB-Code would be installed first.
Also, it might occur if your BB-Code add-on was installed first but it does not add its table BB-Code to XenForo's BB-Code Manager, only as plugin code.
Even though the newly installed add-on appears to work instead of VaultWiki's table BB-Code, which BB-Code gets used might be random each time the code-event listeners are rebuilt (such as when upgrading an add-on like you did with VaultWiki). In order to avoid this situation, you must manually disable VaultWiki's BB-Code or change the BB-Code tag name that it uses. I see you have opted to disable the VaultWiki code.
When VaultWiki is installed or upgraded, if it is adding its BB-Code new, it checks if there is already a BB-Code in XenForo's BB-Code Manager matching the same tag name. If there is already one from a different add-on VaultWiki will use a different tag name for its own BB-Code. This is the best that we can do in this situation, and is already more than most other add-ons do.
Marking this as Working as Designed.