I am just learning about all this myself, appears sky3ds has a template file that tries to inject header support automatically? If so, I would try to inject a header on your own with gateway rom patcher v1.0, should be easy enuf to find and use. there are great tutorial threads on gbatemp for it. this 1.0 from what I understand can insert a public header for you...and then try it on a untrimmed rom, I am guessing you are using a scene rom? is your sky3ds the original or blue button?