Firsly, running Can and Abel on your "daily use PC" isn't recommended, meaning that you should have a test PC that you can install various tools on without any anti-virus, personal firewalls and anti-malware. Your anti-virus is doing exactly what it's supposed to be doing: detecting/deleting malicious software.
Secondly, I'm not sure what you mean by messing up your computer, what Cain and Abel tools did you run? I have Cain and Abel installed on a test XP SP2 machine (using VMWare) with no anti-virus, no anti-malware etc.. and the machine boots fine, everytime.
All men by nature desire knowledge.