Answering my own question: The problem didn't really have anything to do with libtool (although it was revealed when building packages that used libtool). I had updated gcc and g++ to 4.8, but cpp was still at 4.6.3. After installing cpp-4.8 the problem is fixed.
Just for the record, the following should work fine for upgrading gcc to 4.8 on ubuntu 12.04:
$ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
$ sudo apt-get update
$ sudo apt-get install gcc-4.8 g++-4.8 cpp-4.8
$ sudo update-alternatives --install /usr/bin/cpp cpp /usr/bin/cpp-4.8 100 \
--slave /usr/bin/g++ g++ /usr/bin/g++-4.8 \
--slave /usr/bin/gcc gcc /usr/bin/gcc-4.8