"The mod identifies which entities it needs to monitor at the beginning of each run, so anything you build after a run has begun will not be included in the results."

Does this mean it identifies the entities when you hit the play button? Or when you load your save? I.e. do you need to save/load each time before you start monitoring?

A run refers to the period of time that you're sampling the consumption of any single ingredient. It starts upon hitting the play button (or when PA advances in the queue to the next scheduled entry) and ends when you hit the stop button or the monitoring period ends. So if you have four entries in your queue and hit the play button, you will be executing four independent runs, one after the other.

The mod maintains a list of all crafting entities that it updates upon your building or deconstructing them. What happens when you start a "run" is that it identifies which of these entities has a recipe that consumes the queried item and is therefore worth monitoring during the sampling period. It's done this way as a performance optimization, because, as long as you're aware of that caveat (and don't change relevant recipes during runs), it won't lead to any inaccuracies.

You definitely DON'T need to reload your save to refresh entities or anything of the sort.

Great! Thanks for the answer. This seems like a super helpful mod for those big packs like pyanodons and such!