When jQuery conflicts with other libraries like prototype, it's
usually because of the dollar sign notation. There's a "no conflict"
function build into jQuery that you can use to get around that
documented here:
http://docs.jquery.com/Core/jQuery.noConflict
Basically it takes the dollar sign notation away from jQuery (which is
shorthand anyway).
Before noConflict: $("#id")
After noConflict: jQuery("#id")
Don't know if that helps you in this case -- don't know much about the
MS JS lib -- but it sure has gotten me out of some tight spots! (If
you use this, just remember to find-replace all the dollar sign
notation in your JS...)