I had this issue when working with a SU model that included an imported component (a 2d figure) set to it's own layer, so I could control it's visibility in different scenes. Telling the 3d view in LO to zoom extents on scenes that included the figure was partially cutting off the figure. Turned out that something had gotten wonky in the SU model (scenes would not update properly - layer visibility would not update, even though I checked that box in the update dialog). I ended up deleting, then re-creating the scenes - that seemed to fix the issue in both SU and LO.
By the way, Barry - I am absolutely loving Layout. This is the second proposal I have put together using it, and it saves immense amounts of time over exporting all my views to VectorWorks. Tell everybody working on it that they rock, would you?
I'll try to work up a list of suggestions and wishes for you, too.
Mark Leichliter