The defined shell under "Preferences/Default Settings"
cannot saved with the dialog "Save Defaults", if there
are some shell-commands defined in nedit.rc.
I have made same tests and it seems the problem is,
that the variables from "shell" and "shellCmd" are
perhaps to similar at a specific point (or false code).
In the result of the function translatePrefFormats()
the variable TempStringPrefs.shell points to the first
shell-command of TempStringPrefs.shellCmd.
You find my notices in the patch marked with "JOO".
Perhaps you will find another/better solution, then
give it back.