Definition:
Malware: short for malicious software, is any software used to disrupt computer operation, gather sensitive information, or gain access to private computer systems.
If you install malware on your computer (either by accident or on purpose) you run the chance of having ANYTHING happen to your computer. All it takes is a "Hacker" that has good enough code writing skills to write a script, imbed it into a file that you download (you thinking it is something legitimate), and you install said program or file. Once that is done, the script that was written can stop your security program from working correctly, and give the "Hacker" access into your computer. Once the "Hacker" has access into your computer, he (or she) can do whatever it is that they want. They could change all of your settings for every program you have installed, could install new programs without you knowing, and much more. So to answer your question, Yes a "Hacker" could change your Limewire Settings. I would suggest that if you are worried about someone gaining access into your system, then you need to either make sure you have good Firewall / Antivirus / Anti-malware software or stop using P2P software.