XFree86-start-menu-icons path problem

["Dr.D.J.Picton" <dave at aps5 dot ph dot bham dot ac dot uk>]

I went into the start menu, clicked Programs/Cygwin-XFree86/editors/emacs.

No response. (I had started the X11 server!)

So I looked at the properties of the emacs shortcut, and simulated the
operation in a command window:

cd c:\CYGWIN\bin
c\:\CYGWIN\usr\X11R6\bin\run.exe emacs

This failed to work. Typing just 'emacs' revealed the problem - the system
could find the /bin DLL's but not the ones in /usr/X11R6/bin.  Appending this
directory to the path then made the start menu icons work:

set path=%path%;c\:CYGWIN\usr\X11R6\bin

A similar change to the system path enabled the start menu icons to work.
But is it a recommended practice to include Cygwin directories in the standard
system path?  (It makes it easier to launch Cygwin applications from a 
Windows environment, but I'm worried about potential side effects).  In my
view it would be preferable for the path setting to be handled by the 
shortcut.