Я попробовал собрать и собралось без проблем (коммит fecda6853d9bbc3b6df13e48cb0283e7c8ab7d52 последний на данный момент):
localhost:~/test-build/bitcoin-0.9.0$ dpkg -l |grep libboost-syst
ii libboost-system-dev 1.49.0.1 amd64 Operating system (e.g. diagnostics support) library (default version)
ii libboost-system1.49-dev 1.49.0-3.2 amd64 Operating system (e.g. diagnostics support) library
ii libboost-system1.49.0 1.49.0-3.2 amd64 Operating system (e.g. diagnostics support) library
localhost:~/test-build/bitcoin-0.9.0$ gcc --version
gcc 4.7.2
Copyright (C) 2012 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.