depends on how you have fraps set up... if you limit the fps you will often get more lag but if you dont you will get a huge variation in fps if you have a low end cpu.
dont bother recording at full rez always use half. or better still dont use fraps use bandicam or quobi. bandicam enables a more even spread across the cpu cores so it doesnt affect the fps as much. quobi im about to try for the first time myself.
hmmm forget quobi it has a 30 second max record and watermarks.