[patch] Fixes the issue for me.

patch (text/plain), 343 bytes, created by igrek on 2013-02-11 02:30:25 UTC

--- a/diffuse-0.4.6.ebuild	2013-02-11 13:05:26.000000000 +1100
+++ b/diffuse-0.4.6.ebuild	2013-02-11 13:02:29.000000000 +1100
@@ -30,7 +30,8 @@
 
 src_install() {
 	"$(PYTHON)" install.py \
-		--prefix=/usr \
+		--prefix=${EPREFIX}/usr \
+		--sysconfdir=${EPREFIX}/etc \
 		--files-only \
 		--destdir="${D}" \
 		|| die "Installation failed"