So I started a new game, saved at the first point, exited, then renamed the srm to srm.bak for safekeeping, then uploaded and renamed the srm I wanted and it worked.
Any ideas why this is an issue? I'm not really complaining, I'm more intrigued at this point. It almost seems as if the emulator keeps track of whether or not a save should exist. That seems counterintuitive considering the concept of removeable memory cards on the console itself and I would assume an emulator would not need to care if a game had ever been started. Is it similar to modern consoles where it tracks and creates an internal memory file of the game existing and has save files separate?