The PEP 446 partially fixes this issue. The issue #19764 should fix it completly. Since you are using Python 2, you should not wait until the issue is fixed, but work around it.

To workaround the issue: use you own lock around the creation of processes. Example:
---
lock = threading.Lock()
...

def run_command(...):
   with lock:
      proc = subprocess.Popen(...)
   return proc.communicate()
---

The problem is that a thread B may inherit the handle of a pipe from handle A because the pip is marked as inheritable, and the subprocess module must use CreateProcess() with bInheritHandles parameter set to True to be able to redirect stdout.

Said differently: the subprocess is not thread-safe, you have to use your own lock to workaround race conditions.