Hi - saw this thread about CUPS, I've seen the same problems since a recent upgrade, I don't think it's a permissions issue.  The clue is in this error message:

"/etc/cups/${EPREFIX}/usr/libexec/cups/filter/commandtops"  file not found

The string "${EPREFIX}" is appearing in that file name unexpanded; i.e. rather than treating EPREFIX as an environment variable, CUPS is actually looking for a directory literally called "/etc/cups/${EPREFIX}".  This looks like an install-time bug.  I will file a Gentoo bug report if it's not already filed.  But, in the meanwhile, there's a very hackish workaround:

#  cd /etc/cups
# ln -s /  '${EPREFIX}'   # quotes needed!

which will create a symlink

lrwxrwxrwx 1 root root    1 May 13 18:11 /etc/cups/${EPREFIX} -> /

After this, the path

"/etc/cups/${EPREFIX}/usr/libexec/cups/filter/commandtops"  

will resolve to /usr/libexec/cups/filter/commandtops

and you should have a working CUPS again.

Just a workaround hack, not a nice solution!  

Hope this helps,

  - Charles