Forgive me if I posted this twice (new to google groups).
I just had the same problem - I uninstalled j2re-1_3_1_08-windows-i586
and reinstalled and thereafter, IE 6 would exit after 10 seconds or
so.  I reinstalled j2re-1_3_1_08-windows-i586 again(without
uninstalling) and the problem went away.  Coincidentally, I am having
problems with popups and have just started using AdAware.  Maybe it is
a combo of both java and adaware?