This Bmesh based boolean setup brings wrong results compared to Carve. It's a typical use case from a visualization project.
Tested with the official Blender release on Windows 7 64
I'm doing architectural visualizations so I often use boolean operations to create flexible and changeable setups of facades in case architects change their minds about a design during the project. When using booleans on a regular basis on complex stuff like me then it is inevitable to recognize that the Bmesh booleans are still inferior to those of Carve. Since I assume that Carve is a library you would like to drop at some point in the future, I would like to express my concerns that this must not happen until Bmesh booleans are at least as reliable as Carve is. This should really be a condition from my point of view as a user, some people have to work with it after all.
Anyways, I have great respect for your work and I'm willing to provide more bug reports on the matter until this target is reached. Consider this only being the first one.