Symlinking libltdl into a project (as in) libtoolize --ltdl is pretty stupid when later on aclocal decides it needs to run in libltdl/ -- it'll try to write in the aclocal.m4 file that can be reached through the symlink, instead of removing the symlink before writing. This may happen in the non-subpackage case (whenever that'll work), but I believe it can also trigger when AC_CONFIG_MACRO_DIR is shared between the packages.
Bug in aclocal? I think so. Cheers, Ralf