It looks like this will happen if VaultWiki's DIV/SPAN BB-Codes are disabled when you convert BB-Codes, or if DIV/SPAN BB-Codes are nested. Also if some DIVs are nested, and others are not, a mismatch will occur for un-nested DIVs.
Since DIV/SPAN are disabled by default in VaultWiki (or at least the VaultWiki version of their functionality), you'll need to go to VaultWiki > Wiki Code Manager and enable them before converting in order to avoid this issue.
Also, according to the bug I mentioned last night, content in NOPARSE should not be removed, but NOPARSE itself would be removed.
Fixed the DIV issues for the next release.