Anyone else having issues with rust.io rcon not authorizing connections even when privileges are granted in uMod and ingame? Also not showing the loot and buildings overlays? 

As far as i know the RustIo config does not have anything to do with connections, you would go to RustIO servers
(http://playrust.io/) page and type in the name of the server, The map will come up and you log on using steam , I always create a shortcut to the map on my desktop which makes it easier to use it when playing.

I think Rust.IO might be having permissions issues with identifying steam users as admins for the map webpage. I am identified as an owner on the gameserver itself through my SteamID and name. I am also identified as a uMod admin within the permissions system as well. 

It is extremely weird. I can "toggle" admin view on the Rust.IO server webpage and see all player positions but cannot see the loot or buildings layers. I also cannot access the rcon console via Rust.IO webpage. When I try to use the "console" feature through Rust.IO, it connects for a split second then gives me a 1000 error saying "not authorized".

what browser are you using, i had to switch the firefox because, loot and building layers did not work

406Gromit

what browser are you using, i had to switch the firefox because, loot and building layers did not work

I am using firefox on both pc's (seperate steam accounts) and can log into through steam with no problems, make sure you have optioned to view those things in the config,json

{
  "apiKey": "************************************",
  "broadcastChat": true,
  "broadcastDeaths": true,
  "broadcastSpawns": true,
  "defaultLanguage": "en",
  "displayBuildings": false,
  "displayMonuments": true,
  "displayMortality": true,
  "enableLocationSharing": true,
  "helpMessage": "To locate yourself on the LIVEMAP, browse to <color=#CC3A2D>http://playrust.io</color> and type in ************ !",
  "hideSpecificMonuments": [
   ],
  "welcomeMessage": "To locate yourself on the LIVEMAP, browse to <color=#CC3A2D>http://playrust.io</color> and type in *********** !"
}

I am sure you have added yourself to the users folder as an owner , i cant think of anything else that might be blocking it.
Even though i have disabled showing buildings on the map i can still see the option to view them as an admin.