Please never call autotools directly, instead use eautoreconf (or eautomake, and JUST THESE TWO) from autotools.eclass. If you have any reason why those don't work, please let me know to fix them.
New version (1.5.9) was just added to the tree. Ebuild is ~arch, and package.masked, so bug can be closed.
Oops, discard previous comment. Obviously it was posted to the wrong bug.
Fixed in CVS. No revision bump.