Having just gone through that waffly description of the problems and various levels of fix, I think there are really only two fixes worth considering;

1) Make Popen instances fully threadsafe. Give them a recursive lock attribute and have every method acquire the lock at the start, and release it at the end.

2) Decide the "try to reap abandoned children at each Popen" idea was an ugly hack and abandon it. Remove _active and _cleanup(), and document that any child process not explicitly handled to completion will result in zombie child processes.