I think the AABox/AABox sweep intersection test is broken (Intersection.h, line ~90).
For example it is clear to see that the test will always report an intersection if the relative displacement of the boxes is (0,0,0). The implementation on Gamasutra referenced in the comment has the same problem btw!
Trigger false positive in unit test
Proposed fix
Second version with corrected overlap test
I posted a second version of the patch that fixes an incorrect interval overlap test I introduced in the first patch.