I encountered the same problem.
I notice our WSDL (generated from .net) contains a namespace that is associated with 13 different prefixes. The elements missing in the xml happened to be elements using these duplicate namespaces. As a quick test I edited the wsdl and changed the elements namespace prefix to the last of one defined, then retested in soap ui and the elements then were kept in the xml view. I think soap ui may have a limit on how many times a namespace can be assigned a different prefix.
I think our WSDL should have a better definition. However the developers are beholden to .Net and I doubt Microsoft will be making improvements soon. So it would be helpful if SOAP UI could handle the condition.
