How to close small I.E. browsers

In our case, Selenium script start executing with Application1 and depending upon the status being displayed in one of the screens, it has to open the Application2 and perform the approving process by entering values into four different text fields and sign-out from this Application2 and then control should comes back to Application1 and clicks on the Refresh button and continues with the execution.

Everything is working as expected. But after clicking on each text field in Application2, small I.E. windows are opening and they are not getting closed.

We are unable to even get the window handles of these small I.E. browsers.

We have also tried methods like killByName and taskkill. When these commands were used, all the I.E. browsers are getting closed abruptly and causing failures in the Grid.

We usually run huge volume of test scripts on Grid and when such commands were used, all the actual running I.E. browsers are getting closed along with the small I.E. browsers.

When we manually execute the test cases, we noticed that whenever we input the values into the text fields of Application2, a small flash like thing is opening and closing immediately without any manual intervention. But with the selenium scripts, the small I.E. browsers are not getting closed.

We are suppose to open our applications on I.E. browser only as these apps support only I.E. browser.