I has this happen to me quite a while ago.
http://forum.world.st/old-windows-in-image-not-responding-td3922341.html

As well as the suggestion there, you might also try...
    SystemWindows allInstances [ :w | w delete ].

cheers -ben

Johan Brichau wrote:
Hi there,

I often get in a situation where 'ghost windows' remain in the Pharo window (see screenshot).
These windows are closed (see taskbar) and I cannot select nor click these ghost windows to remove them.

Is there a way to remove them programmatically?
They cause visual clutter when working with multiple real windows and I do not want to rebuild an entire development image each time this occurs.

Though this is in Pharo3, I think I occassionally had these in Pharo1.4 as well.

cheers
Johan