You seem to have the correct command line (more examples in the ds rom ripping link in my signature if you need them).
Anyhow make sure you are using the .nds version or strip the GBA header from the .ds.gba version (everything before 200 hex if I recall).
If the makefile is anything to go my DSFTP seems to use NDSTools filesystem as opposed to another (a lot of filesystems exist as well as the abililty to use none at all (all integrated into one binary)), if that does not work all I can guess is the DLDI patching somehow messes it up which is unlikely.
As for a different checksum different versions of ndstool make for different sums and I can imagine you are using a different version to the author.
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