Yes I was having the same issue as well.Now I know I'm not going mad, further to this, the last time I checked it didn't seem as though the real NAND game saves were extracting to emuNAND properly either, in the individual game options.
Ah I see, currently using d2x-v10. I could always go back to good ol' trusty v8 and test. Which I shall do.Hmm, maybe it has to do something with the d2x cios then...
My personal experience is everyting is working fine with emusave, not counting the known problems, like Zelda SS.
I am still usin D2X v8 (249 w. base 56, 250 w. base 57)
Edit: However it was working with D2X v-10 before so I don't see why I would have to use v8, but I'll test regardless just in case.