Same problem

[gillesvds]

@EarlyOut
I experiment the same problem with my own flex web site.
However, this website works well with IE9 : www.harmoniamundi.com but
I do not know why. It seems using exactly the same settings as mine.
Do you make any progress ?

[EarlyOut]

No, I really don't know Javascript. In particular, I don't have the
tools/skills to step through a script to debug it, and I'm not sure
I'd know what I was looking for if I did.

I will probably start looking in other directions for help, and I'll
certainly post back if I find an answer. Using the X-UA-Compatible tag
does take care of the problem for me, but I really, really don't like
to put in hacks to accommodate a current browser!

[EarlyOut]

I still don't know how to fix swffit.js, but there two workarounds
that seem to do the trick.

The first is the one I've already mentioned, forcing the browser into
IE8 emulation mode with a meta tag:

<meta http-equiv="X-UA-Compatible" content="IE=EmulateIE8">

The other is with a bit of CSS;

body {
overflow: hidden;
}

That gets rid of the vertical scrollbar in IE9, and has no ill effects
on other browsers, as far as I can tell.