I've still been seeing a problem with my keybinding categories being corrupted when I load both Archy and ARH.  In troubleshooting this, I decided to completely remove my WTF folder so that the game would create a new clean copy.  I also deleted all other addons except these two. And the problem still occured with multiple characters. It didn't make any difference if I used character specific bindings or not.  The glitch is VERY easy to reproduce.

I found a thread on wowace from July of this year during the Legion beta that seems to be talking about this exact same issue.  

https://www.wowace.com/addons/bartender4/tickets/1229-key-bindings-legion-beta-corruption-see-image/

I think this is what's happening with ARH.  Can you PLEASE look over this thread.  The last page explains exactly what the fix is.  It has something to do with how key binding categories and labels are defined.  I looked at the main .lua file for Archaeology Helper and I see that the bindings are done programatically.  I don't know enough about lua or wow scripting to be able to understand what's going on.  But I can't help but suspect something is amiss here.  

Anyway, please go to the last page of that thread and just take a look.  Maybe it will help in resolving this issue.