>> operating system:
XP SP3
>> python version:
2.6.2
>> waf version (or svn revision):
1.5.6
>> observed output and expected output:
default.cache.py:
LIB_BOOST_FILESYSTEM = 'boost_filesystem-vc90-1_39'
LIB_BOOST_PYTHON = 'boost_python-mgw44-1_39'
LIB_BOOST_SIGNALS = 'boost_signals-vc90-1_39'
LIB_BOOST_SYSTEM = 'boost_system-vc90-1_39'
LIB_BOOST_THREAD = 'boost_thread-vc90-mt-1_39'

expected:
LIB_BOOST_FILESYSTEM = 'boost_filesystem-mgw44-mt-1_39'
LIB_BOOST_PYTHON = 'boost_python-mgw44-mt-1_39'
LIB_BOOST_SIGNALS = 'boost_signals-mgw44-mt-1_39'
LIB_BOOST_SYSTEM = 'boost_system-mgw44-mt-1_39'
LIB_BOOST_THREAD = 'boost_thread-mgw44-mt-1_39'

notice -mt everywhere (the safe choice.) this should also be a
configuration option (boost comes with several variants - mt is
multithreaded, -d is debug, those can be combined to form -mt-d. list not
exhaustive.)

>> how to reproduce the problem?

store all boost libs in one place (on windows, boost\stage\lib) and use

    conf.check_tool('boost')
    conf.check_boost(lib='signals filesystem python system thread',
           kind='STATIC_BOTH', 
           score_version=(-1000, 1000),
           tag_minscore=1000,
           mandatory=True

>> testcase - how to reproduce? (provide attachments for testcase files)