When entering a manual invoice (by using Artio VM Invoices -> Create new invoice) I am not getting the correct item price for each item I add. The item price is the Net price but If I have set a discount on that price this is not calculated. This is a serious issue for me as I have over 5000 products in my db and I have discount for all of them!

VM Invoice takes the basic net price from VirtueMart DB table.

There exists a lot of types of discount in VirtueMart - which one are you reffering to? Discount based on customer type? Volume discount? ...

Each item in products table has one product_discount_id that refers to product_discount table.

This is what I mean. This is the main Product discount

If you try to edit an order through the base virtuemart interface you will see that this discount is used (I know that also other discount exists but this is the most common)

Okey. We will add this feature to next release. Thanks for noticing that.