Operating system and graphics card
OS: Microsoft Windows 7 Professional
Graphics: Nvidia GeForce GTX 750 Ti
Broken: (example: 2.69.7 4b206af, see splash screen)
Both working and broken in same blend file.
Short description of error
Two cubes with similar object to modify/boolean difference one subtracts the other intersects on subtract. May be bug.
Exact steps for others to reproduce the error
Based on a (as simple as possible) attached .blend file with minimum amount of steps
I believe (and yes, as a code developer myself I hate that I'm not sure, but would claim 99.5% confidence) I made a cylinder named Hole.Inside.1st by remeshing, starting with a plane, and reducing to a single vertex, then by snap to vertex an existing cylinder creating the both end circles of another object, extruding edges until two circles were drawn, then using Loop Tools bridged the two circle loops to create a cylinder. The second is a simple mesh cylinder with the same number of verts and dimensions.
It seems to me that there is little difference to remeshing a cylinder, duplicating all vertices and bridging them to create the walls. In the end, I have created a manifold consisting of 2 ngon circles, which by bridging have edges for the sides and making a cylinder mesh. The first is a manifold that looks like a cylinder in almost every way (apparently) but is not the same some how. This object does not modify boolean subtract properly and acts like an intersection instead. Both the cube and cylinder for each pair exist with boolean difference modifier (not applied) in the same .blend. One works, the other doesn't. Both look the same and I think technically should work. There are no non-manifolds or all four objects are manifold.
Here is an external link to the file: http://www.pasteall.org/blend/36702
and the attached file: