CC @theuni
On Ubuntu 13.10 (GNU/Linux 3.11.0-14-generic x86_64), autogen+configure fails thusly,
$ ./autogen.sh && CXXFLAGS="-O2 -Wall -g" ./configure --without-qt --with-incompatible-bdb
...
checking for main in -lminiupnpc... (cached) yes
checking for boostlib >= 1.20.0... yes
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system... yes
checking whether the Boost::Filesystem library is available... yes
configure: error: Could not link against boost_system !
config.log says
configure:10798: checking whether the Boost::Filesystem library is available
configure:10822: g++ -c -O2 -Wall -g -Wall -Wextra -Wformat -Wformat-security -Wno-unused-parameter -Wstack-protector -fPIE -fno-stack-protector -fstack-protector-all -DBOOST_SPIRIT_THREADSAFE -DHAVE_BUILD_INFO -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -I/usr/include conftest.cpp >&5
configure:10822: $? = 0
configure:10836: result: yes
configure:10993: error: Could not link against boost_system !
git bisect located the problem commit as being efdfee423f23df88ffa4b846e4522419fb081ce1