I had this problem some months ago, where XFree86 (4.0.1 IIRC) would
sometimes reject connections, giving an error message of unknown magic
cookie, under 2.4.0 but not 2.2.something. strace of the X client
shows that the cookie was in fact sent correctly.
This must have been a bug in the X server. Upgrading to 4.0.3 fixed it
(but perhaps there is a regression or it is not really fixed, only masked?)
I still have no idea what could be the cause.
Olaf
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