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Cygwin/X settings are configured primarily through command-line parameters passed to XWin.exe. Cygwin/X comes with a file called startxwin.bat that launches an X Server, a terminal, and a window manager.

XWin.exe command line parameters

[-nodecoration] [-[no]trayicon] [-[no]winkill]

XTerm problem

1) My xterm shows, but the rest of the screen is covered in ugly grey. Or I get twm.
Solution: if you are running "startx", change the contents of "/usr/bin/startx". 
Hint: see what happens if instead you run You'll probably 
get something simpler. So you can do:
  mv /usr/bin/startx /usr/bin/startx.orig
  ln -s /usr/bin/ /usr/bin/startx
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