Vangaris Being "logged in" does indeed refer to the new client only - Riot did not integrate their replays into the legacy client, so our tool can only retrieve them if you're logged into the updated client.
The replay of the match you played with LoLReplay2 running should be available regardless though. Do you have replay recording enabled? Do you have any files in "...\Documents\LoLReplay2\replays"? For the next match you play, does it already create an entry for that match while you're still playing?