Mcebuddy runs the custom commands directly and not though a shell. CMD extension is only supported by a shell environment and not a process environments. Try changing the extension from CMD to BAT or invoke the CMD script from a batch file and it should
work.
Also your raise a good point on the location of custom commands. Custom commands are very complex and advanced functions. Putting them in the GUI would be an overload. Hence the decision to put them on profiles.conf. Anything in mcebuddy.conf needs to
be accessible through a GUI.