I hope it's not a problem, Mike. I have a similar problem. If I'm playing minor pentatonic, I can tell you if I'm in boxes 1, 4, or 5, but am not sure when I'm in boxes 2 or 3. When I'm playing major pentatonic, I don't think in terms of boxes but more in terms of what major shape I'm playing (C-shape , A-shape, etc). I think I've done that way for a couple of reasons. (1) When I first learned to play, I taught myself the C, G, and A major scales down in the cowboy chord area. (2) If I'm playing in E and am swapping between (or trying to swap between) major and minor sounds, the 12th fret right-facing E minor pentatonic is the G-major shape (box 1) and the left facing E major pentatonic is also the G-major shape. In my head, it seems to keep the mental gymnastics to a minimum...minors are boxes, majors are shapes. But, in reality, they're the same boxes and shapes just in different areas.
I think I heard Griff mention a long time ago that the ultimate goal is to not think boxes but just play relative to the root. The boxes are just the ends to the means. So, using that rationale, so long as you know where the root is and what you're playing around it, does knowing the box you're playing really matter?
And, as I sit here and think about it, you should suggest this as an AAP session. I'd really be curious to hear what Griff thinks.