Are both sites operating the same version of PHP and VaultWiki? I don't see a difference that would account for this in the autolink parser between 4.0.26 and 4.1.0 Beta 2 when I diff the files. The only difference could be that the two sites are XF 1.x vs XF 2.x, which would invoke the autolink parser differently; yet I still don't see how the result would be different since the inputs are the same and the parser is the same. I would have to look at this more closely if you can open a ticket.