We just noticed,

The Revit L-Angle.rfa Family from Structure 4 deleted a parameter from the Structure category called "Angle (default)" where you could specify a degree rotation. (which we did in our model)

Then we upgraded to Revit 2008 and then loaded in L-Angle.rfa Family from Structure 2008 (and this parameter is gone), which rotated a bunch of other angles and we didn't notice it until the RFI came saying, "how do we build your angles like this?" We then looked at the sealed documents and then said woops.

In short, if you had built Revit models back in Structure 4 and need to upgrade, make sure you set your rotation to 0 degrees and then correct them a different way so when you upgrade to Structure 2008 or Structure 2009 and want to load in the "new L-Angle.rfa" family it doesn't screw up you older model.