Minecraft runs slow, but high fps?

When I play Minecraft, it runs choppy. I usually get around 200 fps but for some reason it still looks slow. Then sometimes out of nowhere it runs really really smooth.

My system specifications.

CPU: Intel Core i5 4460 (4 cores)
GPU: Sapphire AMD R9 290 (4GB)
RAM: 8GB
PSU: Corsair CX600

At the moment I am using Linux Mint, but I still had this problem in
Windows 8.1
Added (1). I get this problem with and without optifine.

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