Jake,
Have you checked to make sure you are running the latest service pack, at least 4.
I recently upgraded to VW09 and was having the same problem. My position are on their own layer and fixtures on another. When I converted a file from 12.5 to 2009 and start working in it I could not control where the fixture landed. But if I convert and save as a 2009, close and then reopen. I don't have that problem, if my fixture lands near the cross VW is letting me choose which pipe to assign it to. I don't know why but it is letting do it. Oh, also our positions are locked which my be part of it because with them locked the auto numbering does update automatically. Once I place my fixture I have to unlock the pipe, cycle the auto numbering command and then renumber. It is a little cumbersome but I have not find a way around it.
I understand the irritation, I like my lightwright export to be clean and predictable.
Later,