Shark: when you use neopowerkit in NDS mode with a NDS ROM that does not have a proper GBA header that specifies the size of the ROM file, NPK assumes the ROM takes up the entire cart. NPK is not meant to be fancy, it did not allocate anywhere to store ROM files that do not have the proper size in the GBA header/loader.
Look to the author of the app you are using, or preferably use dsbuild to add a gba loader that does take into account the size of the nds file (this will not work with dipstar as far as I know, as dipstar needs unadulterated low level access right from the get go).