Extra oddness is that in the history window it says the filename rule was applied to one of the files but the file itself only has the directory ruled tabble.

That’s the db corruption I talked about in the previous comment.

I guess I’m wondering how/when each rule is applied; Last created rule applied first and down the list, first created to last, alpha?

I apply rules from first to last. But I’m not sure the list always reflects the internal order.

Anyway you are facing a bug. Now that the bug is fixed, the order should be irrelevant.

And second; Are there circumstances when a rule is applied that either the old tabbles are stripped or the file’s tabble list is initialized (which would clear the list as a side effect)?

Clear the list as a side-effect: it sounds like the bug I’ve fixed. 🙂

Does the one-click pop-up possibly block any other rules being applied to a file?

No it does not.

Also, I notice that even if I have the checkbox marked to have the one-click box pop, only the first file seems to get the pop-up.

I couldn’t fill your screen with popups, so there’s a logic that says "there can’t be more than a one-click-tagging popup visible on screen". To see all the files, you should bring up the window called "auto-tagging history".