I've had similar problems and I haven't been able to fix 'em yet.
As it stands on my machine, if i click on a link in an email (or wherever) while in OS 9.0.4, my computer
attempts to launch IE but then quits (the IE icon appears on right side of the menubar). If I have IE open already, the link will work correctly.
Additionally, I've lost the ability to open Outlook. I've deleted it, reinstalled it -- it just won't open. I had installed the beta of Outlook last month (or earlier) and it worked for about a month then it too fails to boot.
I'm just waiting for my copy of Mac OS TenTen to arrive and then I'm gonna reformat. That'll show it!