It sounds like auto linking of the library is picking up the wrong one.
Auto-linking uses #pragma comment(lib, <name>) to specify the library
name needed for linking. It doesn't specify a directory location for
the library, only its name.
Do you have your library search path set to the location of the x64
libraries?
You can verify the library is x64 with dumpbin:
D:\Code\boost\boost-trunk\stage\lib>dumpbin /all libboost_unit_test_framework-vc110-mt-gd-1_54.lib |find /i "machine"
8664 machine (x64)
8664 machine (x64)
8664 machine (x64)