If you have recently upgraded your Magento version to 1.9.3 and are facing issues like

1) Orders are not coming through to OrderCup

2) Order notes are not fetching as expected

3) Shipment information not getting updated at Magento 

This seems to be a known issue with 1.9.3 version of Magento, You will need to make a few changes to Abstract.php in Magento to fix the issue.

You can find the details the changes you need here