Issues moving Codigniter from Windows server to Linux based server

I have moved a CodeIgniter based site from a Windows based server to a Linux based server. I have had various issues. Currently I am stuck on images failing to upload. (server timeout error - about 3 seconds after upload finishes)

Steps taken: Set uploads folder to 777. Try php 5.4 & 5.2. I was looking for a suspected temp folder somewhere, but not finding one. I have searched, and found an article discussing CodeIgniter timing out after 300s. But in my case, it times out almost immediately upload is initiated. File attempting to upload is 41kb.
I have checked php settings, max_input_time: 60, upload_max_filesize: 64M, post_max_size: 64M
Base url & path changed: must be right, the whole site works except for uploading images in admin area.

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