You might have an unclosed BB-Code tag somewhere in that article. Unclosed tags can cause unusual issues, such as disappearing content. The final behavior might depend on which tags were left unclosed.
You mention that some H=1 tags are treated as H=2. There are a couple of reasons for this; however, consistent with the last paragraph, H=1 will be demoted to H=2 if it is not a root-level tag (has any open tags surrounding it). This prevents broken HTML and potential security issues when H=1 is used in that context.
You must also keep in mind that the way the parser worked in VW3 is not the way it will work in VW4, especially now that you have migrated to XenForo. XenForo's parser is wildly different from vBulletin's parser; some things that worked in vBulletin might not work in XenForo. Likewise, some things that worked in VaultWiki 3 will simply not work in VaultWiki 4; however, we try to limit these differences to issues that affect security.
I cannot know the specific situation in your site's bug report, because it refers to a wiki page that I cannot access.