||We deploy ArcGIS Explorer (900) to a large number of users within our organization, and we constantly encounter this issue when fielding data and/or application updates to our users. I don't think there is one solution to the "Basemap contains one or more invalid layers" error, because it can happen in a number of circumstances. Here's the steps we take to try & resolve the invalid layers issue. So far (knock on wood) it has worked for us:
1) Has any of my data recently been updated? Delete the map cache either through AGX or manually in Windows Explorer
2) Have my service/layer connections changed or are they still valid? Manually add each service (including ESRI online services) listed in the basemap/default map NMFs through the button to verify.
3) Is my basemap/default map obsolete or corrupt?
Delete or edit the basemaps.
4) Have I done anything that might have generated accessed multiple AppConfig entries? Accessing different NCFGs in a Dev/Test/Prod environment, double-clicking an NCFG file, and typing the AppConfig path into AGX (Globe Button-Set Application Configuration) may create separate entries in the AppConfig directory of a user's local workstation, and these AppConfig entries may be in conflict with each other. When in doubt, we delete all sub-directories under AppConfig. Every entry under the AppConfig directory could contain separate Basemaps and AddIns.
5) When all else fails, delete the settings.xml
A bit daunting, but we've largely alleviated this burden by putting in place some automated processes (i.e. cache delete, AppConfig delete) that run after any major update to our users. It has greatly reduced the number of users who encounter layer errors.