Overview: The problem is how to prevent/block external alteration of my START MENU and FAVORITES Folders by intrusive webpage scripts/cookies/apps that could potentially affect my system in more dramatic ways.

Detail: My system has been bypassed while on the internet, even with an IDS and Personal Firewall in-place. Miscellaneous links and/or groups of links have been placed in my Favorites Folder and even within the Windows START MENU Folder. I am not certain which webpage(s) are at fault. Subsequently, I have not seen any source code that would indicate a culprit or that could be used to develop an effective counter.

Bottom Line: Is there a way to unilaterally block this method of intrusion into my system?