Why do I get hiccups when a new GFX or article is loaded for the first time?

[Eternal Yoshi]

The games I played run at 60FPS(60VPS in Dokapon's case) at all times.... except when I spawn a new GFX or article for the first time.

Things like new menus/spells in Dokapon Kingdom, Mewtwo's Shadowball in Melee, and Hadouken and it's derivatives in Tatsunoko vs Capcom cause the game to hiccup for half a second, but only for the first time loading the thing. Why is this?
I've had this issue no matter what version I used but for the sake of discussion, I've moved to 5.0.
Why is this happening and how do I get it to stop?

I attached images of my settings in the Graphics tab if it helps, and my Laptop's specs are basically;

Operating System: Windows 8.1 x64
Processor/CPU: Intel Core i7-363QM CPU@ 2.40GHz
Video Card/GPU: Nvidia Geforce GTX 660M
Memory/RAM: DDR3 6.00 GB RAM
Dolphin Revision Currently Using: 5.0

[KHg8m3r]

Shader cache generation. Its a problem we know of and are working to find a good way of fixing. Just keep playing your games, and don't switch versions too quickly as the shader cache is build dependent.