Well, I finally had this happen to me on a rush job. I have yet to get it figured out, but did find that life became a little easeier when I entered the command: "synchronizereferences". This did not kick me to model space like the other ways to synchronize, and worked pretty quickly so I could just use the command and plot. Unfortunatly I have to do this every time I want to plot the sheets. Good luck
The post that Jeff_M linked above touches on the cause of the problem. We found the cause of the problem not long after I posted on it last time, I just haven't been back to the boards to share.
The problem is caused with a file is Xrefed into your drawing containing a surface and pipe network that is also Drefed into your drawing. My theory on it is that the Xref loads first and the drawing thinks the Dref is already loaded because it sees it in the Xref. The problem started in 2012 SP2.0 I believe, and it remains up through 2013 SP1. I have not checked 2014 for the issue yet, but I'm crossing my fingers that it's fixed.
Currently the only work around we have is to unload the Xref that contains the objects that Drefed and not synching in your file. From most of my testing, it appears that this is only happening when the Xref contains Pipe Networks, but it affects surfaces and alignments in the drawing you are trying to do the work in. If you've already setup sheets (let's call this Plans.dwg) that have both the Dref and Xref objects, then I would recommend opening that design file (call this 3D.dwg) that contains the pipe network, Save As something else (call this 2D.dwg), delete all pipe networks and alignments, and finally Xref 2D.dwg into Plans.dwg. From this point forward avoid putting Objects that you wish to Dref in files that you will need to Xref.
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