System Information
Archlinux
Nvidia GTX 460

Blender Version
Broken: 10f4c26 (2.7 RC)

Short description of error
Creating a boolean modifier setup with two planes boolean joined subtracting from a cylinder (see http://blender.stackexchange.com/a/7285/599 for context) does not give the same result when created different ways. Using a cube gives the expected result, while directly adding planes does not.

Exact steps for others to reproduce the error
In the attached .blend

• layer 1: Boolean operation set up by adding planes
• layer 2: Boolean operation set up by adding a cube

Exact setup steps:

For planes:

1. Add plane
2. R+X+90
3. G+X+1
4. Add plane
5. R+Y+90
6. G+Y+1
7. Add boolean join modifier to plane 1 with plane 2 as target
8. Add cylinder
9. Add boolean difference modifier to cylinder with plane 1 as target

For cube:

1. Add cube
2. Move cube with snapping so one edge is in the world center
3. Delete top and bottom vertices on the edge opposite edge in the world center
4. Select one of the remaining two faces and separate by selection
5. Add boolean join modifier from separated face to other face
6. Add cylinder
7. Add boolean difference modifier to cylinder with separated face as target.