1.) Which precise "12c" version?
2.) Have you already tried stripping the objects of their permissions and re-applying them?
Have you got any hidden pages? When I first tried 12c I noticed a bug with dashboards occurring if you had hidden pages located anywhere except as the last pages. I can't remember exactly what was happening now to be honest but I think it was other pages not appearing.
Ours is 184.108.40.206.0.
Ya I tried removing and re-adding the roles but that also din't help.
Yes we do have many hidden pages which are placed at the last. We tried to re-order the pages but no luck.
If you create the dashboard by hand again in 220.127.116.11.0 I imagine everything works fine, right?
Can you do that for one of your dashboard with the problem and then compare the "dashboard layout" file between the upgraded version and the one you created by hand?
It's the file that exist inside the dashboard folder for each dashboard as it's the one listing the pages, order etc.
Use the Catalog Manager to see the XML code of the file.
Any difference there inside?