Many users of high speed cameras often ask about the difference between framing rate and shutter speed (aka exposure time). Both are to do with time, and to a certain extent there is a dependancy of one on the other, so I can fully understand where the confusion comes from.
In short, frames per second indicates the quantity of distinct images that are captures every second of recording, and shutter speed (or more accurately, exposure time) is the amount of time that each individual image is exposed to light. So, in the picture, the width of each square wave represents exposure time (shutter speed), and the frequency of the waves represents the framing rate (fps).
Take a look at this document for more information. It also includes advice on what settings to choose. Of course you can contact the IDT guys if you have further questions.