Hi there,
I've got the same problem to, my site is freshly installed.
Running on 1.3.8a. The orders are showing on the admin homepage. But not on the customers/orders page. I've checked the database and the orders that are missing on the orders page are definitly in the database. I spend a lot of time finding a solution for this problem on the zen-cart forum.
I've read that there are known issues with paypal and that there is even a paypal addon for viewing abandond orders.
I am not using Paypal however I am using Multisafepay for dutch customers. I checked if that the callback url was correctly configured in my multisafepay account and it was. I even copied a new orders.php to my shop but no succes:(
I hope someone can put me in the right direction for a solution, I'm stuck.
Kind regards,
Rayring