This problem still exists in version 5.

For anyone else having this problem, I grossly hacked a javascript fix;

<!-- Inject Script Filtered --> <!-- Inject Script Filtered --><script language="javascript">function pause(mil) { date = new Date(); var cDate = null; do { var cDate = new Date(); } while (cDate-date < mil); }</script><script language="javascript">pause(1000);window.focus();</script>

It essentially "pauses" the popup window, giving time for the parent window to finish stealing focus (even when cuteeditor is set to not have focus) and then refocuses the popup window. Crude, but effective.