I'm going to assume you're using FlashME v8a? Which if you check the official download site for it, it even says that DS link is reported to have problems with this version.
I would suggest you try a previous version (v7) if it will still be compatible with your DS that is, or just wait for v9 or whatever the next version will be called, as that'll most likely have a fix for it.
Official FlashME Download Page.
