It may have an issue, more so having a subdomain or alternative domain name using the same webspace may. I think vbSEO sets the base to be your default domain and as such all relative URL's will be relative to the "base" set.
Ideally you would be able to stop this happening in you alternative style (if it's a style forced by this plugin which isn;t usually selectable by users it would make no difference to your SEO as it would never get crawled anyway)
I've not used vbseo, but I'm sure a vbseo plugin which sets teh base directory could be modified so it can work with this add-on.
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