Tricky bug. Threads were playing with a mutable, non-local variable.

theengineear · theengineear · commit 859564d1df3d · 2014-09-18T17:10:02.000-07:00
Just shallow copy the dict instead and things are OK.
diff --git a/run.py b/run.py
@@ -615,7 +615,7 @@ def process_model_worker(leaf, language, model):
         del leaf[language]
     init = get_init_code(leaf, language)
     try:
-        plot_options = leaf['config']['plot-options']
+        plot_options = dict(leaf['config']['plot-options'])
     except KeyError:
         plot_options = {}
     plot_options['filename'] = leaf['id']
