First the kills stopped counting and I got stuck at about 1253 kills. Then I installed a beta version of the game and counting started again, but each time a small amount of the total kills was counted.

Then I found that if I turned the whole game off and on and played only 1 endless game (until they killed me), then everything counted right.

1. Install the beta version of the game.
   
   
2. Start the game and play any endless map.
   
   
3. As soon as the red guy kills you, press ESC and end the game via "quit.exe" in the main menu.
   
   
4. Start the game and repeat the previous points until the achievement appears on your screen.

Feel free to ask any questions, I'll try to answer them.
I hope this helps, let me know in comments.