You've got something wrong obviously, but it's completely unrelated to the battery install. All you're doing with the battery relocation is just lengthening the stock cables from the stock attachment points, so it is exactly the same as having the battery under the hood in the engine bay. Look elsewhere for the source of your problems...

Actually, I guess I should qualify that.. If you did the battery relocation correctly, that won't be the problem. This assumes that you haven't removed something (like a ground, etc) that is needed for proper operation, and have attached the power cable to the correct location, etc.