Hi,
I did not use multibib yet, but as far as I can see, an additional call to bibtex is needed for each suffix defined in the \newcites list. As of now, the plugin calls bibtex only with the main document as an argument.
However, there is a pending pull request on Github by to integrate biblatex which I didn't manage to integrate due to lack of time, but could do it very quickly if needed. As I understand, you can do everything with biblatex that you can to with bibtex.
Moreover, biblatex seems to be much more feature complete and at the same time easier to use than bibtex. I am not sure if it helps with your existing documents, but it uses bibtex as a backend.
Maybe it's an option for you to take a look at it. If not, let's see how we can extend the plugin. :)
Sorry for taking that long to respond…
Best Regards
Carsten