Really long variant directories seem to break the build:

C:\cygwin\home\andrew\Documents\10gen\dev\src\mongodb\src\mongo\base\make_string_vector.cpp : fatal error C1083: Cannot open compiler generated file: 'build\win32\64\cpppath_C_cygwin_home_andrew_Documents_10gen_dev_opt_include_boost-1_53\libpath_C_cygwin_home_andrew_Documents_10gen_dev_opt\release\use-system-all\client_build\mongo\base\make_string_vector.obj': No such file or directory

I don't entirely understand this, since this is not as long as the windows path maximum, but editing the SConstruct and hacking get_variant_dir to return a shorter path does fix the problem.