So maybe you already have.. But have you upgraded the project? Even if you were already on V8i you should enable Integrity Check in the Edit>Preferences dialog. it should run automatically, but if not right click on the project and select revalidate. once the integrity check completes, right-click on the project again and choose Upgrade>From Integrity Check Results. Once this completes, open the project in Administrator and it should upgrade THAT project and add it to the new DB3 file. So, you must do this for each project.
If this is done, maybe check the APCUSTDIR path definition in PROJECT.INI. If it is blank, or shows red.. you may need to adjust it. Not sure if there is something additional required to push it all to the DB3 from the settings.dbf??