The basic build with no DLC only has version 4. Because it was an update of a DLS asset it did get added in the later build as built-in.
Yes, I have come across a few examples like that. And the "odd" packaged asset that seems to have no DLS version at all. I have found that you really need to be running a Trainz version with all your normal DLC content and another one without any DLC to be able to see what is actually going on.
So far the "odd cases" have worked themselves out with subsequent updates.