Yes, if your browser and other OS are using a lot of resources. Computer resources are limited, hence, if other non-Matlab programs are hogging all the resources, then Matlab will slow down - or vice versa - Matlab can slow down all other OS programs.
Check your memory & cpu usage when running your TSP algorithm to see if it's using a lot. Your OS will determine which program gets priority in processing, and thus it's not something you can easily adjust in Matlab.
You could try optimizing Matlab codes that are inefficient (e.g., ones that are growing matrices). Use the matlab Profiler to determine the slow code.
