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The cygwin program run.exe is designed to do just that. It's what I use for this purpose :-) ...
I was using run.exe too. run.exe used to hide the window and the task bar entry. But since my upgrade from Cygwin 1.7.9 to 1.7.15, run.exe only hides the window but not the task bar entry, when invoked from the Startup menu in some cases.
This seems buggy, see my thread: http://cygwin.com/ml/cygwin/2012-07/msg00473.html But I don't have the impression that a developer accepted this as bug.
Do you have a suggestion how to avoid this situation?
I used to have difficulty like that with startxwin, but it does not happen any more for me with xlaunch. It did look like a race condition or something ... Eliot
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