Lag, doesn't occur when fraps is recording

I’m getting a weird lag problem - in a first person perspective game a level that was previously running fine tends to start stalling at a certain point, just for a second, then moving away from that point it seems ok again. It’s just a visual jerkiness for a second, doesn’t affect sound. It seems that it occurs when looking in a certain direction but there doesn’t seem to be anything there that might cause it. When I record with Fraps the problem doesn’t occur! Could be a weird framerate thing? Frames are 120 when the problem occurs then goes to 90 when I start recording.