You seem to mixing your terminology. You talk about "the Run instance's PID", and then "it is enqueued immediately to a thread queue which the main processing loop pulls from." Are you using processes or threads? Or a mix of the two?

When you say "a thread queue", do you mean a Thread::Queue? If so, do you realise that they do not work across process boundaries?

Basically, you need to explain your set up much more clearly. Preferably by posting working code that demonstrates it.