I could not replicate your results, as I understand them. However, I did spend some time on the theory that you are seeing the results of a namespace collision. That is two or more instances with the same name. In my quick & dirty testing, I could not rename the window toolbar, nor the button object it contains. I was able to change the name of the toolbar in the Omnis window.
So it appears there may be a fault in the $name.$assign method for the window toolbars group.