Adobe AIR verses Internet Explorer

We have developed an Adobe AIR application that we point to the URL of our flash web application. We are seeing differences in the communication behavior of our web application with the Adobe AIR container verses Internet Explorer. We are seeing some communication drops fro the Adobe AIR container in our requests back to the web server for requests that take a longer time. Internet Explorer seems to be much more tolerant and handles much better.

Today I was debugging some processing on the web server. I observed that Internet Explorer would wait nicely for my debugging. When I attempted the same thing with the Adobe AIR Container, it fails in the communications.

As I missing some configuration of the Adobe AIR container?