Scott:
One test would be to copy a fill that is working in the good section, switch to a bad section via the Project Map (so the View Settings are not changed) and paste the fill. If the fill changes from opaque to transparent, then I think there is a bug in the file, and you should contact your reseller so Graphisoft can take a look at the file. You could try creating a copy of the section that is working, then changing that section's orientation to match the bad section and see if that fixes the problem. You can also try a
Forward Merge, but this will only copy the model into the new fie, all 2D elements would have to be copied into the new file after the merge.
HTH
David