diff --git a/fuse/ipns/ipns_unix.go b/fuse/ipns/ipns_unix.go
index aa4c8fa5b..b86618c21 100644
--- a/fuse/ipns/ipns_unix.go
+++ b/fuse/ipns/ipns_unix.go
@@ -42,6 +42,16 @@ func InitializeKeyspace(n *core.IpfsNode, key ci.PrivKey) error {
 		return err
 	}
 
+	err = n.Pinning.Pin(emptyDir, false)
+	if err != nil {
+		return err
+	}
+
+	err = n.Pinning.Flush()
+	if err != nil {
+		return err
+	}
+
 	pub := nsys.NewRoutingPublisher(n.Routing)
 	err = pub.Publish(key, k.B58String())
 	if err != nil {
diff --git a/importer/importer.go b/importer/importer.go
index c84dfe3ab..f5f7ce7ae 100644
--- a/importer/importer.go
+++ b/importer/importer.go
@@ -200,6 +200,10 @@ func BuildDagFromReader(r io.Reader, ds dag.DAGService, mp pin.ManualPinner, spl
 
 	if mp != nil {
 		mp.PinWithMode(rootkey, pin.Recursive)
+		err := mp.Flush()
+		if err != nil {
+			return nil, err
+		}
 	}
 
 	return root.getDagNode()
diff --git a/test/sharness/t0080-repo.sh b/test/sharness/t0080-repo.sh
index c2dc851ac..4280ccedc 100755
--- a/test/sharness/t0080-repo.sh
+++ b/test/sharness/t0080-repo.sh
@@ -21,10 +21,16 @@ test_expect_success "added file was pinned" '
 	ipfs pin ls -type=recursive | grep $HASH
 '
 
-test_expect_success "'ipfs repo gc' doesnt remove file" '
-	echo -n "" > empty
+test_expect_success "'ipfs repo gc' succeeds" '
 	ipfs repo gc > gc_out_actual
+'
+
+test_expect_success "'ipfs repo gc' looks good (empty)" '
+	echo -n "" > empty
 	test_cmp empty gc_out_actual
+'
+
+test_expect_success "'ipfs repo gc' doesnt remove file" '
 	ipfs cat $HASH > out
 	test_cmp out afile
 '
@@ -36,8 +42,10 @@ test_expect_success "'ipfs pin rm' succeeds" '
 '
 
 test_expect_success "file no longer pinned" '
+	# we expect the welcome file to show up here
+	echo QmYpv2VEsxzTTXRYX3PjDg961cnJE3kY1YDXLycHGQ3zZB > expected2
 	ipfs pin ls -type=recursive > actual2
-	test_cmp empty actual2
+	test_cmp expected2 actual2
 '
 
 test_expect_success "recursively pin afile" '
@@ -76,8 +84,10 @@ test_expect_success "'ipfs repo gc' removes file" '
 '
 
 test_expect_success "'ipfs refs local' no longer shows file" '
+	echo QmUNLLsPACCz1vLxQVkXqqLX5R1X345qqfHbsf67hvA3Nn > expected8
+	echo QmYpv2VEsxzTTXRYX3PjDg961cnJE3kY1YDXLycHGQ3zZB >> expected8
 	ipfs refs local > actual8
-	test_cmp empty actual8
+	test_cmp expected8 actual8
 '
 
 test_expect_success "adding multiblock random file succeeds" '
@@ -104,15 +114,19 @@ test_expect_success "pin something directly" '
 '
 
 test_expect_success "'ipfs pin ls -type=direct' is correct" '
-	echo $DIRECTPIN > directpinhash
-	ipfs pin ls -type=direct > directpinout
-	test_cmp directpinhash directpinout
+	echo $DIRECTPIN > directpinexpected
+	echo QmUNLLsPACCz1vLxQVkXqqLX5R1X345qqfHbsf67hvA3Nn >> directpinexpected
+	cat directpinexpected | sort > dp_exp_sorted
+	ipfs pin ls -type=direct | sort > directpinout
+	test_cmp dp_exp_sorted directpinout
 '
 
 test_expect_success "'ipfs pin ls -type=recursive' is correct" '
 	echo $MBLOCKHASH > rp_expected
-	ipfs pin ls -type=recursive > rp_actual
-	test_cmp rp_expected rp_actual
+	echo QmYpv2VEsxzTTXRYX3PjDg961cnJE3kY1YDXLycHGQ3zZB >> rp_expected
+	cat rp_expected | sort > rp_exp_sorted
+	ipfs pin ls -type=recursive | sort > rp_actual
+	test_cmp rp_exp_sorted rp_actual
 '
 
 test_expect_success "'ipfs pin ls -type=all' is correct" '