This could be a firmware/flashcart issue, or the possible 1mb save issue. Here is something I posted in another related topic.
"To address your issues, sounds like it's your card. It works fine on my iTouch, my gf's DSTT, and a friends Edge.
About the 1mb save. People here claim it must be 1mb or things will fuck up do to corrupting when too much data is in the 512kb sav. The staff of pokesav said they're just idiots, passing around rumors like idiots do. I personally got passed the reported "corruption" area, after doing things like saving a battle vid, which if the 1mb rumor is true, would of made it easier to corrupt, as they take up ~.2mb . Despite doing this, and some other things I could think of to test this "issue", my game loaded, and saved just fine, on both my iTouch and her DSTT. But to be safe, we both made our saves 1mb.
I'd say fix your .sav to be 1mb, to be on the safe side. And while pokesav says 256kb and 512kb save files, it still works flawlessly on my 1.25mb Platinum save. Who knows who's right, it could be 512kb, and the save corruption could be a card issue."