Hmm... I don't think this is exactly what's happening.  Toby doesn't inject content scripts or use the webRequest API, and only conditionally injects scripts into the page (under which conditions, I don't know).  nytimes.com seems to intermittently be a site it tries to inject into, so I think what happened was on the first visit, it wanted to run, and on the second, it didn't.  I can see this same behavior with Toby by just refreshing nytimes.com a few times.  So we're not granting any permissions, it just doesn't want to run there anymore.  Can you see if that's the case for you as well?

Interesting! Thanks for looking into it. I can't get the run indicator to go away by simply refreshing the page - I tried at least 7 times.

That said, I can't reproduce the original issue any more. Now I can successfully grant access to 1 extension via the refresh bubble, and the Toby extension remains in the "wants to run" state after refresh.

So unless you have other concerns, I think we can just close this as WAI.

I think unless we find new evidence of this, we should close it out.  But let's be on the lookout.

Thanks for filing it!