QA Notice: ... appears to contain PORTAGE_TMPDIR paths
   

Older versions of libtool would incorrectly record the build and/or install directory in the libtool script (*.la). This would lead to problems when building other things against your package as libtool would be confused by the old paths.

You may be able to cheat and use the elibtoolize function in the libtool.eclass. However, if that does not help, you will probably need to regenerate all of the autotool files.