There are multiple buffers between the fraps measure and the fcat measure. The execution context buffer and the vsync buffering. These buffers adsorb the momentary differences of delivery of frames and thus the output frames come out smoothly. The GPU can only work so fast and since its almost always the bottleneck a faster frame wont get processed any earlier so it comes out when the GPU has time, getting delayed in the process. But that frame has now been time shifted, it has a different latency to the frames around it and the contents represents a different time period to when it would be displayed, and that we see as a hitch in the game world. That is different to a frame being displayed too long like in a low FPS scenario but neitherless its still a noticeable effect and we seem to be able to see these things very easily (well most of us can but not all).
The ideal FCAT and fraps output matches precisely, because then we can be sure that all the frames are getting processed with the same latency, which ensures both the content and the delivery of the frames is matched. Of course then what we also want is a perfectly smooth graph for both.
You can actually get the FCAT output to look a lot more like the Fraps output by reducing the execution queue to the minimum (ideally 0 but I think the minimum is 1 on AMD and NVidia these days) while having vsync off. That will actually output quite a spiky graph if the input is also spiky and in addition it will make the fraps output even worse because sometimes the GPU might be starved for work and sit idle.
I am writing about it differently to pcper partly because I have written DX code myself and hence know how this works and partly because NVidia's/AMDs quotes are taken out of the context by them when reporting it. Fraps frametimes matter every bump and hitch is a sign of a genuine shift in animation, but its also a very sensitive measure. On the one hand its right of AMD/NVidia to say that not every little movement is a problem, but its also true that some amount of movement is actually noticeable. What I am trying to do (and have been trying to do for quite a while now) is explain how it works and its impact so people can see precisely what it measures and understand how it works. There is a lot of misinformation on this forum trying to say fraps is useless, but we need both Fraps and FCAT, and we also need a latency tracking tool as well. All of these measures are looking at different aspects of the graphs pipeline and we have a variety of different problems around how the cards currently work.