There is a trick to using Fraps.
Firstly, set the recording resolution to 50%.
Next, you need to find out roughly what FPS your copy of SH3 is running at.
For example, I used to have a ATI 9600 which would pull about 30-40 FPS with max settings so I set Fraps to record movies at 25 FPS and this worked fine.
Just to note there is a little lag when first starting Fraps on low end systems, this quickly goes away in each view.
It will also help to have Fraps save your recording to another drive separate to the one running SH3.
Failing that there is another program you could try, it's called Guncam, not as friendly as Fraps.....
http://www.growlersoftware.com/