Lookups are empty

I have a rule set with two content types A and B.

Both content types have the same parent content type and nothing else more. They are identical except for their name and ID.

I'm adding files to the this rule set with SPFileCollection.Add(string, byte[], Hashtable)

If I add an item with content type A the lookup is working fine. If I add an item with content type B the code runs fine and I get an exception in ULS:

 Stack trace:   
at Microsoft.SharePoint.SPFileCollection.Add(String urlOfFile, Byte[] file, Hashtable properties, Boolean overwrite)    
at Microsoft.SharePoint.SPFileCollection.Add(String urlOfFile, Byte[] file, Hashtable properties)    

Multilookups are working fine. User and Multi user fields too. It's only lookups that don't work.

Anybody have any clue/idea what's going on?