Domino keeps some free white space in its databases, to allow for efficient growth. Compacting gets rid of most of this. Are the servers replicating with other servers? Check to see if the documents are being put back in from another replicating server.
Here's one other option. If you are using Transaction Logging, you also need to specify the "filesize reduction" option when you compact. If you are using a program document to run the compact on a schedule, the place a -B in the command line field. If you are launching it from the Admin client, there is a checkbox. Be aware that this affects your ability to recover the file and apply transaction logs, so it is a good practice to run a backup soon after the compact completes.
I have had the same problem. I found that there were a lot of documents I thought I had deleted in the all documents view. If you chose to remove, rather than delete, they will have remained in the all documents view.
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