In principle, real file system is transparent to applications, and it in charge of platform running as S.O, to manage this thing. So for applications, accessing to a media card, main memory, extended memory.. etc.. etc.. should be indifferent.
Maybe your problem is related with permissions granted to eGPSTrack, can you check if under application management in your mobile, you can find something like "user data access" or "file system access" and check that eGPSTrack has set anything diferent from "not allowed" ?