First off, I think your problem is how your first window is opening. That first window is opening as a "normal window." I think that doesn't have anything to do with any of the "new windows" but I don't know why.

When you say "Subsequent IE windows that are opened" I'm not sure how you're opening them. Do you mean all the new ones opened through the first and/or each successive window, or by the quicklaunch button again.

I would say to try right clicking on the IE button on the quicklaunch bar, and go to properties, then choose "Maximized" under "Run:"

Now, after you open that initial window, and it opens maximized, see how subsequent "new" windows react now.