Also, when you run 'top', look at the 'NI' column. It shows the priority of the process; if the one using up all the CPU has a large 'NI' value (like 19), it means it's running with very low priority. Higher means low priority, lower (down to -20) means higher priority. Don't ask me why
Anyway, as long as the top process is low priority, it shouldn't adversely affect your performance.