Theoretically, the folder structure in your archive should match the folder structure in your mailbox. However, over time, you have probably renamed folders, deleted folders, and moved folders as your worked on your mailbox. The archive does not keep up with all these changes to the mailbox folder structure. Therefore, sometimes items aren't archived where you expect them to be archived. Sometimes you need to use the Find feature to locate archived items.
This issue is more frequent with users whose GroupWise archives date back through numerous GroupWise releases.