diff --git a/src/main/java/org/broad/igv/feature/genome/GenomeManager.java b/src/main/java/org/broad/igv/feature/genome/GenomeManager.java
index 41f227fc7..8c6177ae5 100644
--- a/src/main/java/org/broad/igv/feature/genome/GenomeManager.java
+++ b/src/main/java/org/broad/igv/feature/genome/GenomeManager.java
@@ -234,15 +234,19 @@ public void setCurrentGenome(String genomePath, Genome newGenome) {
         if (IGV.hasInstance()) {
             IGV.getInstance().goToLocus(newGenome.getHomeChromosome()); //  newGenome.getDefaultPos());
             FrameManager.getDefaultFrame().setChromosomeName(newGenome.getHomeChromosome(), true);
-
             loadGenomeAnnotations(newGenome);
             IGV.getInstance().resetFrames();
             IGV.getInstance().getSession().clearHistory();
 
-            PreferencesManager.getPreferences().setLastGenome(newGenome.getId());
+            if(newGenome != Genome.nullGenome()) {
+                // This should only occur on startup failure
+                PreferencesManager.getPreferences().setLastGenome(newGenome.getId());
+            }
+
             if (PreferencesManager.getPreferences().getAsBoolean(Constants.CIRC_VIEW_ENABLED) && CircularViewUtilities.ping()) {
                 CircularViewUtilities.changeGenome(newGenome);
             }
+
             IGVEventBus.getInstance().post(new GenomeChangeEvent(newGenome));
         }
     }
diff --git a/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java b/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java
index 3ce550622..c4c87db37 100644
--- a/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java
+++ b/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java
@@ -38,7 +38,7 @@ public JsonGenomeLoader(String genomePath) {
     public Genome loadGenome() throws IOException {
 
 
-        try (InputStream is = ParsingUtils.openInputStream(genomePath + "..")){
+        try (InputStream is = ParsingUtils.openInputStream(genomePath)){
 
             String jsonString = ParsingUtils.readContentsFromStream(is);