I think i have come to the root of the problem where we was having problems uploading large files to site. It was the max_execution_time, it was set low. I have increased this to 15 mins, so if your file takes longer than 15 mins to upload, then the chances are it wont upload at all. (This will have to be done through ftp)

max_execution_time - This sets the maximum time in seconds a script is allowed to run before it is terminated by the parser.