diff --git a/payu/cli.py b/payu/cli.py
index 6f60805b..745a2937 100644
--- a/payu/cli.py
+++ b/payu/cli.py
@@ -119,6 +119,12 @@ def set_env_vars(init_run=None, n_runs=None, lab_path=None, dir_path=None,
     if reproduce:
         payu_env_vars['PAYU_REPRODUCE'] = reproduce
 
+    # Pass through important module related environment variables
+    module_env_vars = ['MODULESHOME', 'MODULES_CMD', 'MODULEPATH', 'MODULEV']
+    for var in module_env_vars:
+        if var in os.environ:
+            payu_env_vars[var] = os.environ[var]
+
     return payu_env_vars
 
 
diff --git a/payu/experiment.py b/payu/experiment.py
index 9628ad47..b2bacd56 100644
--- a/payu/experiment.py
+++ b/payu/experiment.py
@@ -237,9 +237,11 @@ def load_modules(self):
         loaded_mods = os.environ.get('LOADEDMODULES', '').split(':')
 
         for mod in loaded_mods:
-            mod_base = mod.split('/')[0]
-            if mod_base not in core_modules:
-                envmod.module('unload', mod)
+            if len(mod) > 0:
+                print('mod '+mod)
+                mod_base = mod.split('/')[0]
+                if mod_base not in core_modules:
+                    envmod.module('unload', mod)
 
         # Now load model-dependent modules
         for mod in self.modules: