A 3rd gen Intel i7 CPU, an ATI 7xxx GPU, 16 gigs of RAM, Win7 64 bits
Broken: hash ebf9d31
Short description of error
In cases where a lot of islands are being subtracted from a low-poly volume, missing faces can develop in all three boolean modes. You should see a result like this...
Exact steps for others to reproduce the error
Open the .blend and invoke the new boolean tool with the selection, it shouldn't matter if you use difference, intersect, or union