Fuse position, in theory, should have much less to do with transmitting power as it does keeping your car from burning down! The reason to keep it close to the battery is just so you dont cut thru/arc out/ect a unfused section. I witnessed a car burning to the ground at the theater by my house due to a person trying to steal the stereo and dropping the pos cable to ground when he took off. Not gonna have a good day
I would make for sure that all the wire is the proper guage and especially that you have a good ground, or better yet redundant grounds. If it works well inside, it is definately power related! Somewhere...