Steps to reproduce:
In practice:
1. Add a tasklist (wnck-applet) to the panel.
2. Open Mathematica.
Result: window list becomes unresponsive and wnck-applet consumes 100% of CPU.

Since developers may not have access to a copy of Mathematica, I will attach a
short C program which has the same effect.
Having traced wnck-applet with gdb, I believe this program triggers the same bug
as Mathematica.

Stack trace:
Not applicable; this isn't exactly a crash.
(It is in spirit, since the user is forced to kill the applet.)

However, the problem is occuring at libwnck/tasklist.c: 1930 (as of version 2.12.3):
  /* FIXME: check for group modal window */
  for (active_window = wnck_screen_get_active_window (screen);
       active_window && !active_task;
       active_window = wnck_window_get_transient(active_window))
    active_task = g_hash_table_lookup (tasklist->priv->win_hash,
                                       active_window);

Both Mathematica's splash screen and the test program's window set their
WM_TRANSIENT_FOR hint to point to themselves, so this loop never terminates.

Other information:
References to the Mathematica problems:
http://forums.wolfram.com/student-support/topics/10215
http://www.ubuntuforums.org/archive/index.php/t-76347.html
In particular, there's a workaround for now.