Ok, Hope this wasn't posted already, but I searched through the forums and couldn't find any mention of it. It was something that took me a bit to work out and hopefully this'll help some of you having the same problem. Basically I was trying to use a backup save game I took from my original game cart and use it with my Cyclo DS. problem was, the Cart wouldn't load it. I did all the checks made sure it had the same name and all that and nothing. But the game still had levels unlocked, which showed it was accessing data from the save game file. Turns out, I had downloaded a US version of the game ROM, whereas mine is a Europe version. So I ripped my own flash cart (the europe version) and it worked. Like I said it took me a few days to work out and I hope this helps some of you. Make sure the region of the ROM matches the region on the save game.
It is good that you posted this but this should be common sense that the save game should match the ROM that it came from. Considering the European and US ROMS for the same game have different numbers, this makes perfect sense. This is why leaving the number on the ROMs is a good idea.
Ah, that's what those numbers are for. Cool. Never knew that. Well, I thought it might help someone, I just found it weird that it was clearly accessing the save game data, but couldn't load it fully.