Mixing use of autotools-utils.eclass with regular phase functions and/or random econf/emake calls is unsupported and it never was. And in a near future, it will cause fatal errors during the build process. Please fix it by using correct autotools-utils phase functions as pointed out in the example on top of the eclass and/or its manpage. If you have any trouble, feel free to ping us and we'll help you fix it. Thanks.
Fixed in CVS.