You can check with bjam --debug-configuration
It appears that it does find user-config, but then it says it doesn't see the relevant feature: $ bjam --debug-configuration notice: found boost-build.jam at /Users/me/Dev/company/projects/ThirdParty/boost/boost-build.jamnotice: loading Boost.Build from /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2 notice: Searching /etc /Users/me /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2 /usr/share/boost-build /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/kernel /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/util /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/tools /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/contrib /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/. for site-config configuration file site-config.jam . notice: Loading site-config configuration file site-config.jam from /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/site-config.jam . notice: Searching /Users/me /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2 /usr/share/boost-build /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/kernel /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/util /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/tools /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/contrib /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/. for user-config configuration file user-config.jam . notice: Loading user-config configuration file user-config.jam from /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/user-config.jam . notice: OSX version on this machine is 10.6.2 notice: will use '/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin/gcc-4.2' for darwin, condition <toolset>darwin-4.2.1~iphone/<architecture>arm/<target-os>iphone/<macosx-version>iphone-3.1.2 notice: will use '-arch' for darwin, condition <toolset>darwin-4.2.1~iphone/<architecture>arm/<target-os>iphone/<macosx-version>iphone-3.1.2 notice: will use 'armv7' for darwin, condition <toolset>darwin-4.2.1~iphone/<architecture>arm/<target-os>iphone/<macosx-version>iphone-3.1.2 notice: will use '-mthumb' for darwin, condition <toolset>darwin-4.2.1~iphone/<architecture>arm/<target-os>iphone/<macosx-version>iphone-3.1.2 notice: will use '-fvisibility=hidden' for darwin, condition <toolset>darwin-4.2.1~iphone/<architecture>arm/<target-os>iphone/<macosx-version>iphone-3.1.2 notice: will use '-fvisibility-inlines-hidden' for darwin, condition <toolset>darwin-4.2.1~iphone/<architecture>arm/<target-os>iphone/<macosx-version>iphone-3.1.2 /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build/feature.jam:485: in feature.validate-value-string from module feature error: "iphone-3.1.2" is not a known value of feature <macosx-version> error: legal values: /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build/property.jam:276: in validate1 from module property /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build/property.jam:301: in validate from module property /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build/property.jam:310: in property.validate-property-sets from module property /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build/toolset.jam:151: in toolset.flags from module toolset /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/tools/common.jam:430: in common.handle-options from module common /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/tools/darwin.jam:132: in darwin.init from module darwin /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build/toolset.jam:38: in toolset.using from module toolset /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build/project.jam:881: in using from module user-config /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/user-config.jam:40: in modules.load from module user-config /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build-system.jam:257: in load-config from module build-system /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build-system.jam:399: in load-configuration-files from module build-system /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/build-system.jam:554: in load from module build-system /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/kernel/modules.jam:283: in import from module modules /Users/me/Dev/company/projects/ThirdParty/boost/tools/build/v2/kernel/bootstrap.jam:142: in boost-build from module /Users/me/Dev/company/projects/ThirdParty/boost/boost-build.jam:17: in module scope from module