Can you please provide a small, complete, compilable sample application that demonstrates this so we can investigate further?
For example I am unable to reproduce this error with this simple application:
<s:Button label="Open" click="import mx.managers.PopUpManager;PopUpManager.createPopUp(this, NewPanel)"/>
I ran into the same issue, and the root cause was that PopUpManager/PopUpAnchor would not properly set the focusManager if the component being popped up does not implement the IFocusManagerContainer interface. After implementing such interface, the problem goes away.
You may read this blog post (http://eastmond.org/blog/?tag=popupmanager) that inspired the solution.