[eluser]Aken[/eluser]
First, try not to intermingle raw PHP w/ CodeIgniter functions, as CI will often add its own proprietary code on top of PHP. Just look at the set_cookie() method in the Input class.
Second, after you switch to using all CI code (what I would recommend), verify your cookie settings in your config file. Make them as basic as you can - use just lowercase letters, make sure the cookie domain and such is accurate.
I don't have IE so I can't completely test anything, but I would start there. I'm guessing there is a setting somewhere that IE treats somewhat differently that is being confused due to the inconsistent use of CI vs. PHP. Give it a shot, see if anything changes.
