Git status shows modifications after cloning

Hello,

After cloning from a local repository, a git status shows me that each file in the repository has been modified - I don't want this to happen. I have searched around the net, and there is stuff about this happening if the configurations for the original and the clone are not the same, with specific mention of the variable core.autocrlf. However, this variable is unspecified in both repositories, and the differences in config files is listed below.

Origin:
[core]
	repositoryformatversion = 0
	filemode = true
	bare = true

Clone:
[core]
	repositoryformatversion = 0
	filemode = true
	bare = false
	logallrefupdates = true
[remote "origin"]
	fetch = +refs/heads/*:refs/remotes/origin/*
	url = /home/ruggeddoc/Documents/Primary/InstallationGuides/RuggedBackbone
[branch "master"]
	remote = origin
	merge = refs/heads/master
[branch "jateeq.2010-03-08.09-49"]
	remote = origin
	merge = refs/heads/master

I haven't tried unsetting the logallrefupdates (I want to log updates). Does anyone think this is a config file issue? If it is, any idead on how to solve it? If not, what can I do so that git status, or git diff do not show modified files right after cloning?

NOTE: On the origin, the only branch that exists is master, whereas after
I'm done cloning, I create another branch and then checkout that branch's
head right from the start. 

Thank you for your help, Jawad