Do you use the latest release of DevitkitPro and do you also use Ahezard's libnds because I can't build the bootstrap with Ahezard's libnds and DevitkitARM R45I only do make and get the bootstrap file. Also fyi I've tested the "two" bootstrap files. When you run "make" you get a nds-bootstrap.nds and if you run build-cia.bat yu get a bootstrap.nds. I've tested both XD
Just remember to rename to release-bootstrap.nds or unofficial-bootstrap.nds!