The issue is that the resetWindows.bat file deletes file named workbench.xmi, but does not include the correct path for the stand-along config tool which is:
C:\Program Files (x86)\Aware IM Configuration Tool\bin\workspace.metadata.plugins\org.eclipse.e4.workbench\workbench.xmi
I manually deleted workbench.xmi to straighten out the windows.
It's too bad that they get screwed up in the first place. Managing the config tool windows in general is a crummy user experience.