It shouldn't be 100%, since you are using a dual core, but 50% at most, for BC, but considering your normal usage is 20%, it may just as well appear to be 100% after BC is running.
Do all missions have this problem?
What is on screen when it slows down?
And does the memory graph go up as well?
BTW, BC will try to claim as much CPU as it can get, on a dual core, that is 50%.