I can't make any sense of this report.

In configdialog.py, the DynOptionMenu self.optMenuKeysCuston is set in LoadKeyConfig (line 1066) by
            itemList = idleConf.GetSectionList('user', 'keys')
            itemList.sort()
            if not itemList:
                self.radioKeysCustom.config(state=DISABLED)
                self.customKeys.set('- no custom keys -')
            else:
                self.optMenuKeysCustom.SetMenu(itemList, itemList[0])

or the same without the 'if' clause.  This code was not changed by the patch.  Nor was config.IdleConf.GetSectionList.  So there should be no way for anything to appear on that menu unless in the user keys file.

To test Veky2 as posted, I added it to my user keys files.  I opened a IDLE fresh and brought up the config dialog.  Veky2 was on the list and when I selected it and closed the dialog, there was no problem.  I tested and the Veky2 definition of <<dedent region>> as <Shift-Key-Tab> worked.  (I just added that to Terry.)  When I opened the dialog again, Veky2 was still there, selected.

In the absence of a failing test case or of any idea how the code could produce the behavior you report, there is not much I can do.