Flex app behaves differently when Adobe automation files loaded

We have an application built with Flex 3.1. I am attempting to create QTP tests for this application. The instrumentation files are loaded at run time, not compiled into the application.
I am using QTP 9.5 with the Adobe Flex Add-in 3.0. I am able to see the controls an run tests to some extent.
The main issue I am trying to resolve is that there is a difference in behavior of the application when it is started with the instrumentation files. The differences occur both inside and outside of the QTP environment.
The observed differences are:
The initial page is a login screen. After entering the id and password, I can click ‘Enter’ or click the “Log in” command button. With the instrumentation files loaded, the ‘Enter’ key no longer works.
When I log out of the application, a progress screen displays while the environment clean-up occurs. When the progress bar hits 100%, the original login screen is displayed. With instrumentation files loaded, activity stops when the progress bar hits 100% and the original login screen is never displayed.
After logging in, a window with perspective tabs displays. Each perspective tab page contains a window containing a list of resource associated with the perspective. When instrumentation files are loaded, the tab pages exist, but the perspective windows are not created.
I realize I am dealing with application-specific behavior here and I am pursuing this with our developers. What I am looking for is any information related to differences in application behavior when instrumentation files are loaded.

I can't seem to reproduce what you are seeing with this sample application:
<s:Application xmlns:fx="http://ns.adobe.com/mxml/2009"
               xmlns:s="library://ns.adobe.com/flex/spark">
    <s:states>
        <s:State name="state1" />
        <s:State name="state2" />
    </s:states>
    <s:controlBarContent>
        <s:Button label="change state" click="currentState=currentState=='state1'?'state2':'state1'" />
    </s:controlBarContent>
    <s:Button x="50" y="50" label.state1="state1" label.state2="state2" skinClass="CustomButtonSkin" />
</s:Application>
Can you provide a similar sample application that demonstrates the issue?

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Regards
Vivek

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