With the help of the test script I wrote, he managed to track down the change on the libtool-2.0 branch that fixed the problem. Applying this same change to a 1.5.x release fixed the problem. He has uploaded a new Debian package with the change, and I’ve altered the jhbuild bootstrap module set to include the patch too. The copy of the patch included with JHBuild can be found here. Hopefully it will also be in a future 1.5.x release (assuming that there are any more).
Scott pointed out another case where people might run into the problem is when building binary packages for software. A packager usually builds the new version of the software into a temporary prefix (often by setting the $DESTDIR environment variable when calling make install). If the package includes a library with some applications that link to the library and there is an old version of the package installed on the system, libtool could end up linking with the library in /usr/lib, which could result in a build failure if some new APIs were added. The patch should fix this particular case too.
So if you release tarballs that make use of libtool, applying this patch may help out the people maintaining binary packages of the software for a distro too (assuming that they haven’t gone the scorched earth route and deleted all the .la files …).