I can confirm, I've had similar problems with Civil 3D 2012. Unfortunately the last two times I've seen the problem occured were after I had already signed and sealed the drawing and sent out in a hurry, only to later notice that there are no contours shown on my Drainage Plan or no alignment station labels on a storm structure! We Dref all of our C3D objects from the design files into sheet files and annotate in the sheet file. So far I have seen synchronization issues in pipe networks and surfaces.
In SP1 I had a quirk with a Pipe Network not synchronizing properly when a file was reopenned, and if my CAD tech did not synch the network prior to plotting, the station value on a structure label read ???. I think this problem had to do with reference alignment overrides in the sheet file, as the two structures shared multiple alignments in the design file and I didn't assign an alignment to them. This problem seems to have been fixed in SP2.1. But now, in SP2.1, I have two drawing files that will not display my proposed surface contours unless I click synchronize after opening the file. It doesn't matter how many times I synch and resave, it still will not display upon reopenning the file. I've heard from 1 other engineer in my group who's had a similar problem on a large 500 acre site he's working on... I feel bad for the guy, because those surfaces take some time to synchronize.
I've been rather busy and haven't had time to bring this up with Autodesk support, but I will try to keep a look out for any additional information on this. We're planning to move up to 2013 in the near future, so it may become a moot point and fall off our radar.
