The problem was that I was missing the amazon-envelope part, here is an example of the correct xml I now send to the webservice:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<AmazonEnvelope>
<Header>
<DocumentVersion>1.01</DocumentVersion>
<MerchantIdentifier>A2UAUVMGTII0KR</MerchantIdentifier>
</Header>
<MessageType>Product</MessageType>
<Message>
<MessageID>1</MessageID>
<OperationType>Update</OperationType>
<Product>
<SKU>ABCDORD0005</SKU>
<StandardProductID>
<Type>ISBN</Type>
<Value>9788478888566</Value>
</StandardProductID>
<LaunchDate>2014-03-23T00:00:00.000+01:00</LaunchDate>
<ReleaseDate>2014-03-23T00:00:00.000+01:00</ReleaseDate>
<Condition>
<ConditionType>New</ConditionType>
</Condition>
<DescriptionData>
<Title>Harry Potter and the Philosopher's Stone</Title>
<Brand>brand_item</Brand>
<Description>Harry Potter and the Philosopher's Stone is the first novel in the Harry Potter series, written by J. K. Rowling.</Description>
<Manufacturer>J. K. Rowling</Manufacturer>
<ItemType>sotto_categoria</ItemType>
</DescriptionData>
<ProductData>
<Sports></Sports>
</ProductData>
</Product>
</Message>
</AmazonEnvelope>
And this works just fine, got no returning errors, just note that it takes almost 1 minute for the product to shop up in the seller central, and 10 more minutes for it to be processed and become active. Also, the element StandardProductID is really important, if you don't provide the correct code you will get a missing key error in return.