So I've got a customer who's upgraded drawings from a previous version of Civil 3D to Civil 3D 2013. One drawing contains data shortcuts to pipe networks, alignments, and surfaces. At the drawing open the pipe networks are updated, but none of the other data shortcuts are. Removing the pipe network data shortcuts allows the other data shortcuts to be loaded normally. Using SYNCHRONIZEREFERENCES updates all of the data shortcuts normally in the darwing. So I strongly suspect the pipe networks are the cause of the issue. Opening a new drawing and creating a data shortcut doesn't exhibit the same issues. Also WBlocking the trouble drawing doesn't work either. Any other ideas on a way to fix the drawing?
Does the subject drawing also have the PipeNetwork source drawing as an Xref? If so, unload it and see if that helps. This is what I found (thanks to Jay_B) to fix the multitude of issues I was having with DRefs.