By default, the Collect Full Inventory policy excludes many files and folders. In some cases, the files and folders inside those exclusions are needed.
Here are instructions for ensuring *included* files/folders are part of an inventory. This example assumes the folders needed are everything in "Local Settings" and "Application Data" (both of which are excluded by default.
Please note this will only work for XP machines. You will want to do the *:Users\Public (or other needed file paths) for Vista and W7.