Apparently, the auto-use feature of portage is going away, and the newer versions of portage in ~arch no longer support the "use.defaults" file. However, when using ufed, there is no way to set the flags in make.conf if they are/were set in use.defaults.
ufed 0.40-r1 contains a fix for this, and it was released before portage dropped use.defaults. If there are any particular flags that cause problems for you, please provide details.