diff --git a/auditing.go b/auditing.go
index 67d1faf..94b8c9f 100644
--- a/auditing.go
+++ b/auditing.go
@@ -154,6 +154,11 @@ func NewMerkleTreeBuilder (stack []ct.MerkleTreeNode, numLeaves uint64) (*Merkle
 	}
 	return &MerkleTreeBuilder{stack: stack, numLeaves: numLeaves}, nil
 }
+func CloneMerkleTreeBuilder (source *MerkleTreeBuilder) *MerkleTreeBuilder {
+	stack := make([]ct.MerkleTreeNode, len(source.stack))
+	copy(stack, source.stack)
+	return &MerkleTreeBuilder{stack: stack, numLeaves: source.numLeaves}
+}
 
 func (builder *MerkleTreeBuilder) Add(hash ct.MerkleTreeNode) {
 	builder.stack = append(builder.stack, hash)
diff --git a/cmd/common.go b/cmd/common.go
index e77ec99..6be4fdc 100644
--- a/cmd/common.go
+++ b/cmd/common.go
@@ -226,8 +226,7 @@ func (ctlog *logHandle) scan (processCallback certspotter.ProcessCallback) error
 	endIndex := int64(ctlog.verifiedSTH.TreeSize)
 
 	if endIndex > startIndex {
-		treeBuilder := ctlog.position
-		ctlog.position = nil
+		treeBuilder := certspotter.CloneMerkleTreeBuilder(ctlog.position)
 
 		if err := ctlog.scanner.Scan(startIndex, endIndex, processCallback, treeBuilder); err != nil {
 			return fmt.Errorf("Error scanning log (if this error persists, it should be construed as misbehavior by the log): %s", err)
@@ -239,10 +238,9 @@ func (ctlog *logHandle) scan (processCallback certspotter.ProcessCallback) error
 		}
 
 		ctlog.position = treeBuilder
-	}
-
-	if err := ctlog.state.StoreLogPosition(ctlog.position); err != nil {
-		return fmt.Errorf("Error storing log position: %s", err)
+		if err := ctlog.state.StoreLogPosition(ctlog.position); err != nil {
+			return fmt.Errorf("Error storing log position: %s", err)
+		}
 	}
 
 	return nil
@@ -291,6 +289,10 @@ func processLog(logInfo* certspotter.LogInfo, processCallback certspotter.Proces
 			log.Printf("New log; scanning all %d entries in the log", ctlog.verifiedSTH.TreeSize)
 		}
 	}
+	if err := ctlog.state.StoreLogPosition(ctlog.position); err != nil {
+		log.Printf("Error storing log position: %s\n", err)
+		return 1
+	}
 
 	if err := ctlog.scan(processCallback); err != nil {
 		log.Printf("%s\n", err)