diff --git a/Dockerfile b/Dockerfile
index e3b4c2e..b989670 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -20,6 +20,8 @@ RUN cd /root/ \
  && /root/emsdk/emsdk activate latest-upstream \
  && source /root/emsdk/emsdk_env.sh --build=Release \
  && emcc hello_world.cpp -s WASM_OBJECT_FILES=1 \
+ && python -c "import os ; assert open(os.path.expanduser('~/.emscripten')).read().count('LLVM_ROOT') == 1" \
+ && python -c "import os ; assert 'upstream' in open(os.path.expanduser('~/.emscripten')).read()" \
  && echo "test fastcomp (waterfall)" \
  && /root/emsdk/emsdk install latest-fastcomp \
  && /root/emsdk/emsdk activate latest-fastcomp \
@@ -28,4 +30,3 @@ RUN cd /root/ \
  && emcc hello_world.cpp -s WASM=0 \
  && echo "test binaryen source build" \
  && /root/emsdk/emsdk install --build=Release binaryen-master-64bit
-
diff --git a/emsdk b/emsdk
index e9cbd9d..2544cc5 100755
--- a/emsdk
+++ b/emsdk
@@ -1051,13 +1051,26 @@ def generate_dot_emscripten(active_tools):
   if embedded:
     cfg += "emsdk_path=os.path.dirname(os.environ.get('EM_CONFIG')).replace('\\\\', '/')\n"
 
+  # Different tools may provide the same activated configs; the latest to be
+  # activated is the relevant one.
+  activated_keys_in_order = []
+  activated_key_values = {}
+
   for tool in active_tools:
     tool_cfg = tool.activated_config()
     if tool_cfg:
-      tool_cfg = tool_cfg.replace(';', '\n')
-      if 'SPIDERMONKEY_ENGINE=' in tool_cfg: has_spidermonkey = True
-      if 'NODE_JS=' in tool_cfg: has_node = True
-      cfg += tool_cfg + '\n'
+      for specific_cfg in tool_cfg.split(';'):
+        name, value = specific_cfg.split('=')
+        if name not in activated_key_values:
+          activated_keys_in_order.append(name)
+        activated_key_values[name] = value
+
+  for name in activated_keys_in_order:
+    if name == 'SPIDERMONKEY_ENGINE':
+      has_spidermonkey = True
+    if name == 'NODE_JS':
+      has_node = True
+    cfg += name + ' = ' + activated_key_values[name] + '\n'
 
   # These two vars must always be defined, even though they might not exist.
   if not has_spidermonkey: cfg += "SPIDERMONKEY_ENGINE = ''\n"