Custom Magento 1.3.2.4 fixing - problems with delivery...

In Magento 1.3.2.4 we have installed a couple of modules regarding shipping, delivery and pick up at a store. These modules work together very well most of the time, however, in 1 out 50 orders Magento lacks delivery informations and we want to figure out why and get this fixed. In our checkout we have the possibility to make a delivery or pick up at store. Sometimes users go back and forth, selecting pick up at store, deselecting, selecting a delivery etc. This creates some conflicts in Magento, which results in lack of information in the orders and invoices, and errors sending out emails. This is as you can see custom PHP/Magento work. You will need a high skill of Magento understanding and you must dive into a lot of custom modules for Magento.