I haven't been able to duplicate your environment, but I do know that you can run at least two presesentations at the same time on a single monitor - auto advance tranisitions based on slide timing - and they will continue even if one window loses the focus. Animations, however, wait their turn and will only advance after the next transition/animation is finished, even if it is in another window.
To test this, create a presentation with 3 slides, giving a name of something like "MySlides.pptx". Add some pictures and animations and slide transitions that advance based on timing, not mouse click.
In PPT2007, go to Slide Show | Set Up Slide Show and then under Show Type, click Browsed by Individual. Press F5 to ensure it runs as expected. Press Esc.
Then duplicate the deck, giving a new name of something like "MySlides2.pptx". With both decks now open, navigate to each and press F5. You should see both of them running.
In PPT2010 you can save decks as WMVs, so that may also be an option when it becomes available.