Argh. EA.... There is a bug in the game's replay system. If you watch a replay it saves the replay of that replay in "Last Replay.RA3Replay". If you keep the tool running while you watch that replay at the end the tool saves that replay of the replay again (if autosaving is working properly on your system, and it should). So, you end up with double replays.
This only happens when you watch a replay entirely. If you quit it before it ends it wont be saved.
I wont fix this and release a new beta soon because of it. My tool is working as intended and it's EA fucking up. Although it kinda sucks .