It neither asked for my username/password nor moved the applications to Trash. I also checked the Console and found nothing. I guess there is no way to fix this.
Nevertheless, I was planning to install Leopard from the ground up before this problem happened and it just made me more firm to go ahead with the re-installation.
As for setting stacks icon, I should have done it manually or at least I should have tried applying the workflow to a test folder. Oh, well. I will start using Time Machine again after re-installation of Leopard.
Thanks for taking time to help me out.