Shiptheory downloads Orders from VisualSoft using the GetNewOrders functionality of the VisualSoft API every minute. Orders that are downloaded into Shiptheory are instantly marked Downloaded in VisualSoft. This means that if you have more than 1 integration connected to your VisualSoft store, both using the GetNewOrders functionality, you may find that some orders will be missing from your account as they have been marked Downloaded by another integration before Shiptheory checked for new orders.
VisualSoft are aware of this potential integration conflict and have an item on their roadmap that covers a fix for this. For more information, please contact VisualSoft.
Another point to keep in mind is that the GetNewOrders will only pull down shipments that have the status of Payment Received if your orders are Downloaded and you're wondering why they are not coming through double check that the status is correctly set to Payment Received as anything else will result in the order not being pulled down.
If you've gone through this and still can't figure out why your orders aren't coming through, please don't hesitate to get in touch with support