I've similarly had poor experiences with the Humble ports of games. Off the top of my head I can think of Super Meat Boy, which usually crashes within the first minute, and Psychonauts, which is so broken that it ruins all the fun. Both of these on OSX, by the way, but I've had similar problems on Linux.

This is why I have stopped buying the bundles, even though this one contains games I have wanted to play for a long time.

I have also told the Humble guys this, but I have gotten no response.

In case people are still curious, the upload yesterday was missing a bunch of files. There is a new file for download 9/12/2013 which is working fine for me.