I'm still seeing this in gutsy, and I may have narrowed down the
circumstances when it happens for me (at least in recent memory).

When I've got a lot of things going on (starting up a few applications
like evoution and firefox), gksu will never pop up on the first call.
What appears to be happening is that if there aren't enough resources to
get the gksu GUI up in 5 or 10 seconds, it decides not to do it at all.
It may work the second time because the gksu binary and its resources
are already loaded into the file cache and can fire up the GUI in a
short amount of time.

Now, when I see stuff like  the following in libgksu-2.0.5/libgksu/libgksu.c 
(around line 2577), I get doubly concerned that there may be timing bugs 
causing this problem:
      { /* no matter if we can read, since we're using
           O_NONBLOCK; this is just to avoid the prompt
           showing up after the read */
        fd_set rfds;
        struct timeval tv;

        FD_ZERO(&rfds);
        FD_SET(parent_pipe[0], &rfds);
        tv.tv_sec = 1;
        tv.tv_usec = 0;

        select (parent_pipe[0] + 1, &rfds, NULL, NULL, &tv);
      }

-- 
gksu dies on first run
https://bugs.launchpad.net/bugs/55172
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