Only way that I have figured to fix it is by making these calls in separate iframes, by using iframes it appears to the external application that js is called by a separate page and it processes it.
So,what I am looking for is this:
1)First is there a way to do it w/o using iframe:
//import a 3rd party url(<c:import url='url>) which has this script:
call external js and pass this var
//this is inside my jsp
call external js and pass this new var1
Now my call is ignored if i use say c:import to import first url...if i use iframe it works.
2.Now if i put my js script inside an iframe.
It doesn't work.