Hi Eirik,
I assume that you have enabled the option for "auto-adding MIR Pro" to each new instrument channel in Vienna Ensemble Pro. By deactivating this option, MIR won't be instantiated automatically any longer (see screenshot 1).
... a little-known trick to work with _one_ instance of MIR Pro across multiple VE Pro frames is to use its more "conventional" VST/AU-plug-in version instead of the full-blown, VE Pro based versions. You will lose some nifty features like auto-guessing Instrument Profiles and the like, but you won't need to use seperate instances of MIR in each instance of VE Pro any longer (... assuming that they all reside on the same computer, of course). Just de-activate the respective MIR Pro Preference (see screenshot 2).
HTH,
/Dietz - Vienna Symphonic Library