You are talking about CPU usage but it's not entirely clear (to me) what you mean. I'm guessing you are looking the that windows task manager thingy? You will see 4 graphs (one for each core), is one core at 100% or all? Or is it the bar graph on the left side that is at 100%?

Because if one of your cores is getting 100% load but the others aren't then I would suggest you look at ISBoxer's CPU settings.