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.
Is this a problem with ngrep, or the gentoo ngrep package?
If the latter, then I don't think I'm the right person to assign this to..
I've fixed this removing old ebuilds.