I am having a problem with portage ignoring my USE flags set in /etc/make.conf. /etc/make.conf exists, is syntactically correct, and has correct permissions set. I am not in a chroot environment or anything unusual like that. I have been using this configuration for weeks now with no issues.
portage is only ignoring the flags set in /etc/make.conf. It is not ignoring environment variables from the command line, or /etc/portage/package.use. I am using the default desktop profile, and have not changed anything in there recently.
Here's whats happening when I do 'emerge --update --deep world -p' to illustrate the problem:
localhost ~ # emerge --update --deep world -p