davide, first thing, you made your sheets with 1 pixels between neighbours. Sheets used by MCDedit are not using any spaces.
Second thing, you're using RGB with alpha, the format, which haven't been used for sheets before. So it can't import sheets of this RGBA format properly.
I've reuploaded fixed exe.
But as for "pixel space", and number of tiles per row - it's the thing which I believe would require for some "settings" menu. And for now, you have to change your sheets by removing any spaces, and using exact grid 32x40 pixels.