I identified a way to work around that issue by using an invisible spacecraft.dll powered vessel placed between the INI powered multistage2.dll and the 'link' to the dll powered vessel plus using specific 'focus' settings on both the multistage2.dll INI and in the spacecraft.dll INI (so that the release of the dll powered vessel – with full tanks - from the dummy spacecraft.dll vessel could be done semi or even fully automatic). I think that have implemented that on some of my released but older / outdated pre-Orbiter2010 addons (would have to check). Haven't tested if it still works on Orbiter2010.
If remembering well, I have also written a post about this specific topic on the older Orbiter Forums (M6). When possible, will try to find such post and copy+paste to this thread.
In any case, such kind of workaround (as well some others) might become outdated with eventual future releases of Vinka's multistage.dll and, as noted above, another option could be to use the scenario editor.
António