I've figured out a work around, by not using a custom button and not using the postbackcommand event.  However, I do think you should look into it, as I believe it to be a bug with CuteEditor. 

If you do the following steps you should be able to reproduce this behavior:

1) Add a CuteEditor control to a web form and set it's OnPostBackCommand event to a valid CommandEventHandler.
2) Next, set it's ConfigurationPath property to a valid toolbar config file, which contains a save button with postback="true"
3) Next, add a button to the form and handle it's click event.  In the click event determine what ConfigurationPath is set and toggle back and forth between the current one and a different one that also has a save button with postback="true"
4) After toggling to either toolbar click the save button and see if it calls the PostBackCommand event.

I've been unable to get it to call the PostBackCommand event after toggling to a different toolbar, even if I explicitly reset the event handler after setting the ConfigurationPath attribute.

(e.g.,

if (!cuteEditor.ConfigurationPath.Contains("1st"))
{
 cuteEditor.ConfigurationPath = "~/.../My1stConfig.config";
}
else
{
 cuteEditor.ConfigurationPath = "~/.../My2ndConfig.config";
}
cuteEditor.PostBackCommand +=new CommandEventHandler(cuteEditor_PostBackCommand);

)