Scenery.cfg - Areas disappear after setup

I've recently done a complete uninstall / reinstall of FS9 and have found a frustrating problem with my scenery.cfg that I'm hoping someone knows how to fix. The problem is that after I've installed a scenery and its either been added to the list automatically or manually, it sometimes disappears when I start FS9. FS9 does go through the scenery update messages during the initial load, but when I get into the scenery list, the new additions are missing.Has anyone experienced this? and if so, how can I get around it without doing another install (reinstalling this game takes me about a week because of time constraints and I don't want to do it again unless I have to)?Thanks,Greg