<use> <flag name='qt4'> Install qt4 dependent optional tools (e.g Catalyst Control Panel) </flag> </use> <use> <flag name='modules'>Build the kernel modules</flag> </use> This should be just one big <use/> block with multiple <flag/>s inside. Otherwise, tools reading metadata.xml will be confused. The only reason repoman allows this is technical DTD limitation.
Fixed in x11 overlay
Fixed in the portage tree...