I had turned on the apache2 use flag while doing some testing with Apache2. Once I was done, I uninstalled apache2 and removed the use flag using ufed...the flag was still there when I checked a few days ago and had been a source of many of my problems (see http://bugs.gentoo.org/show_bug.cgi?id=18017 ).
I've sometimes noticed that if you change the location or line number of the USE variables then ufed is unable to compensate for it; the same may apply to download mirrors set by mirrorselect. This is why I use mirrorselect for mirrors and ufed for USE variables and do not edit the make.conf file manually unless I have to change other options.
I don't know if I'll get to this by the end of the package upgrade phase on sunday, but it is in the todo list (I have finals shortly so that's my delay).
I just found that even though scanner isn't checked in ufed no -scanner is put into my USE= line and kdegraphics depends upon scanner (verified with emerge -pv kdegraphics).
It seems ufed is quite the deceitful little application as many have realised already. I had unset many flags including esd and tcltk but they were still very much active and no -esd and -tcltk were entered into make.conf. Basic functionality of successfully adding and removing flags is the least one can expect from the utility. I hope to see fixes and improvements in the near future.
Try the new version. Ufed 0.32 is in portage and addresses many USE flag issues
