I'm using version 1.1. And the savefile that got extracted from the Zelda game cart is 512KB. I haven't tried uploading it to the cart again, but you say it should be 1MB? Then it most certainly wouldn't work afterwards, hmmm... what to do?

And I don't know if size really is the matter here. Mario Kart 7's save file for example is also 512KB, and I didn't have any problems extracting that one. I really don't know.