I found some spare time to look at it. 
Applications started within the session, always  stuck in select, endlessly 
waiting for a response in my case. 

I had prepended a gnome-terminal before xmodmap in Xgl-session. Here is
its backtrace

Core was generated by `/usr/bin/gnome-terminal'.
#0  0xb7fc3410 in __kernel_vsyscall ()
(gdb) bt
#0  0xb7fc3410 in __kernel_vsyscall ()
#1  0xb75fb2dd in select () from /lib/tls/i686/cmov/libc.so.6
#2  0xb70c155a in _xcb_in_read_block (c=0x80a7ca0, buf=0x80a7328, len=8) at 
xcb_in.c:248
#3  0xb70c07fc in xcb_connect_to_fd (fd=3, auth_info=0xbfb79c10) at 
xcb_conn.c:131
#4  0xb70c2f21 in xcb_connect (displayname=0x0, screenp=0x0) at xcb_util.c:279
#5  0xb76d57f7 in _XConnectXCB () from /usr/lib/libX11.so.6
#6  0xb76be109 in XOpenDisplay () from /usr/lib/libX11.so.6
#7  0xb7a1f032 in gdk_display_open () from /usr/lib/libgdk-x11-2.0.so.0
#8  0xb79fca0d in gdk_display_open_default_libgtk_only () from 
/usr/lib/libgdk-x11-2.0.so.0
#9  0xb7bb2e4f in gtk_init_check () from /usr/lib/libgtk-x11-2.0.so.0
#10 0xb7bb2e84 in gtk_init () from /usr/lib/libgtk-x11-2.0.so.0

I also checked if xauth really add the token for Xgl and it works
correctly.

-- 
[Hardy] Race condition in Xgl startup process
https://bugs.launchpad.net/bugs/176515
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Bugs, which is the bug contact for Ubuntu.

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