Your FPS drops when you capture footage in any program.
In Fraps, if you are able to handle what you are "capturing", IE: all units on the screen, graphics, effects, etc., without lagging, you should have a solid 15-25 FPS. If you are unable to capture everything on the screen, because of graphics or too many units, your FPS will stutter up and down. If you are getting 5 FPS, you need to check the settings and make sure Fraps is set to 25 FPS. If it is, and you are still getting 5 FPS, you either (in most cases) 1, need to defrag your HD, or 2, need to get a better system/gfx card that can handle it.
Edit: Just to clarify. I run M&B with 150+ FPS, but when capturing in Fraps, you still drop down to 25 FPS (depending on what FPS you selected in the options) which is considered a "smooth" capture as far as fraps is concerned. You really don't need to select any other FPS than 23-30 but if you have trouble capturing, you can always set the FPS to 15. Anything less than 12 FPS in M&B will not look decent at all.