Index: pym/portage/__init__.py
===================================================================
--- pym/portage/__init__.py	(revision 12696)
+++ pym/portage/__init__.py	(working copy)
@@ -2119,6 +2119,8 @@
 				if ebuild_force_test:
 					self.usemask.discard("test")
 
+		use.difference_update([x for x in use if x not in iuse_implicit])
+
 		# Use the calculated USE flags to regenerate the USE_EXPAND flags so
 		# that they are consistent. For optimal performance, use slice
 		# comparison instead of startswith().
@@ -2189,9 +2191,7 @@
 		# attribute since we still want to be able to see global USE
 		# settings for things like emerge --info.
 
-		self.configdict["pkg"]["PORTAGE_USE"] = " ".join(sorted(
-			x for x in use if \
-			x in iuse_implicit))
+		self.configdict["pkg"]["PORTAGE_USE"] = " ".join(sorted(use))
 
 	def _get_implicit_iuse(self):
 		"""