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.
I've removed obsolete versions, the whole problem is coming down to the usage of "private" function eautoconf in the version 0.6.22-r2.
Problem is that autotools files used in this package are utterly broken and I don't feel like fixing them, especially that I don't have to use autotools.eclass in gnokii-0.6.26-r1 (the current test version). Care to fix them yourself?
P.S. If the other autotools.eclass functions are private, maybe you should consider prefixing their name with _ in the near future. There is no comment in that class that forbids usage of eautoconf.
Offending version has been removed from the tree.
Closed as FIXED.