Your brain is awesome. That's why.
If you play ocarina @25fps for three hours it will be smooth.
If you played ocarina in an emulator @60fps and went back to the original version with the press of a button, you'd be amazed of how choppy it was actually.
It would look smooth again after a while though.
It could also be because of frame pacing. Average frames per second is not a good way to measure these things, because it's not precise enough. It's an average!
One second is a long time for a computer and a lot can go on in those 1000 milliseconds. There's more than one way for a developer to cap their game's frame rate and not all implementations are going to be equal, or deliver the best experience possible.
The best feeling "30fps games" will be those that consistently deliver each frame at or extremely close to 33.3ms intervals.
Example: This graph is of a capture taken from 5 minutes of Wolfenstein: The New Order gameplay. It shows each frame delivered during that time, represented by a tiny square. The frames are pretty evenly delivered, with an average of 60 fps.
Now look at this similar graph from 5 minutes of Far Cry 3 gameplay.
The average frames per second for this segment is 70 fps. This should be better than 60 fps, right? Well no, in this case the Far Cry 3 gameplay will feel far less consistent and stuttery, as frames come in all over the place. Anywhere from 40 milliseconds (25 fps) or greater, down to as little as 8 (120 fps). This problem actually gets worse as you head below 30 fps, because the latencies involved start to become noticeable to the average player pressing buttons on a pad and playing through a TV.
I don't have any graphs with a 30 fps average I'm afraid, but the same will apply. You will see an average of 30 fps for some games, where in fact the frame times could vary wildly. This is what the OP is talking about; essentially 30fps is not always equal, 33.3ms frame times are what he wants.