Inspect every file on your site and determine whether every difference is intended and also correct in terms of both business logic and PHP syntax. Any unauthorized difference should be corrected, usually by replacing with original code or removing whatever didn't come with ZC originally.
Basic outline of steps:
http://www.zen-cart.com/wiki/index.p...Obscure_Issues
This process also empowers you to prepare a list of ways in which your site is different from original official Zen Cart code (and since original official ZC code doesn't exhibit the symptoms you describe, this list will contain important clues to your solution).