Because these tools are meant to deal with source code files and deal with diffs of such files. You are cramming a 1 gigabyte of compressed bits at it and its trying to make sure it could give you a diff of it later on. I don't have any idea why you would want to store it in a CVS type tool if its not going to change that often.. a simple MD5sum of the tar ball and check against that would probably do a check of it.
Remember we have NO clue what you are wanting to do with this or why.. a couple of sentences does not give us enough background on what problem you are trying to solve. You never mentioned 1 gb tar balls or other things.. you mentioned config and script files which update quite frequently.. thats all.
Thank you for the reply. I am going to try checking this file in as a binary using Stephen's cvswrapper suggestion and see if this makes a difference.