It was a fresh install.
I am not sure which is the offending update, but I suspect it is one of the following:
Mac OS X update Combined (Intel) 10.4.8
MacBook pro EFI Firmware Update 1.2
We believe the problem is isolated to the Mac updates. We have one Windows based PC, and the files work just fine on that platform – it is only on the Mac where the problems occur.
There isn’t any set command that seems to trigger the problem. Most often it occurs when we move from a modelspace setting to one of the layout pages (particularly the sections and elevation sheets). The windows and floor slabs will randomly disappear from the view – and will not plot either. They are still there as they show up fine in plan. By changing which layer settings the drawings use, and then changing back to the ‘correct’ ones, we could sometimes get the wayward items to reappear long enough to plot – but sometimes they stayed missing. Likewise, sometimes closing the program down and opening it back up would sometimes give us a temporary cure – but not always, and never permanently.