At many people at the first start of game there is only 1 achievement. If you see that you have only 1 achievement, restart the game, and only when you see that the achievements have really started to fall, fold and forget about it until all the achievements will fall.

What do I want to say? The game has no save file.
Every time you start the game, your achievement count drops to 0 and starts again.
Every time you start the level, your achievement count drops to 0 and starts again.
Every time you leaving the level to the menu and conversely, your achievement count drops to 0 and starts again.
So, just don't do anything, run and roll up the game, go for a walk, go to bed (I did it). And wait, wait, wait...
Sometimes it will seem that achievements have stopped falling again. BUT JUST DON"T DO ANYTHING! They will start falling again.
It will take longer than you think. But in the end you will get your 100%.

And Again: JUST DON"T DO ANYTHING!