Minecraft pulse generator is permanently powered if i toggle too fast

The reason why it stops working is the repeater happens to lock the other repeater when it is powered. Chances are that design was not made to be spammed. A solution I'd suggest is make a fill clock (if you want your construct to be activated every tick all the time) or if you want it to pulse when ever you flick the lever (just like the pulse generator you where using) you can use the second design I listed.

(note: all screenshots are in 1.9 but everything listed will work in 1.8)

Design 1: The Fill Clock. This is when you have 2 commandblocks running a fill command twice every tick, and looks something like this.

The commands the command blocks are running (from top down) are

/fill ~ ~-1 ~5 ~ ~-1 ~ redstone_block

/fill ~ ~1 ~5 ~ ~1 ~ stone

How it works is the top commandblock is run after the bottom commandblock. So the area get filled with stone (unpowering all commandblocks along the blocks) and then instantly replaced with redstone blocks re-powering them all.

Design 2:

So this design uses the same principal as design 1. It will power what you want for 1 tick, and it looks like this.

From the top to bottom the commands are

/setblock 297 91 983 minecraft:stone

/setblock 297 91 983 minecraft:redstone_block

The commandblock to the right has the command /say hi just to prove that the stone block beside it (the block the /setblock targets) does it powered for 1 tick. and it looks like this

Hopes this helps!