File download prompt appears in "Do not close" IE9 window

Forgive me for my lack of Oracle terms because I am not with our Oracle support team.  I am with the general support team.
We are on E-business 11i  We recently upgraded to IE9 and Java 7 update 45. It seems now when users try to export or download a file from a screen the save prompt appears as the typical save bar at the bottom of the IE9 window that is in the background that says "Do not close this window".   This is very confusing to the users.
Is there some settings in IE9 that are causing the prompts to go to that window that no one looks at?

which version of OBIEE/OBIA you are using?

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