Here to chime in with the same problem. I am logged in, I didn't accidentally log out to a guest account: proven in these screenshots. Matchmaking is acting as if I'm 1000 ELO, but the ELO itself on my profile remains normal but acts as if I've beaten (or lost to) a ~1000 opponent. For instance:
My ELO before a battle
The Battle
https://replay.pokemonshowdown.com/gen9doublesou-1732144375-1ndwwtnpmbryau39fjmb5sl39zahn5epw
My ELO after the battle
At one point before I realized this glitch, I ended up losing to a smurf and my real ELO dropped by like 60 LOL rip
My ELO before a battle
The Battle
https://replay.pokemonshowdown.com/gen9doublesou-1732144375-1ndwwtnpmbryau39fjmb5sl39zahn5epw
My ELO after the battle
At one point before I realized this glitch, I ended up losing to a smurf and my real ELO dropped by like 60 LOL rip