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Because of the order of things you did, you now (probably) have what dropbox calls conflicts. These happen when the same file changes in two places. In your case, the metadata.db changed on the new machine before it was successfully synced from the original machine. This happens if you run calibre on the new machine before sync finishes.
The way out of this is probably:
1. Ensure that each machine is connected to dropbox.
2. Go to your dropbox website. Navigate through your folders (on the website) to calibre's library folder, the one containing metadata.db.
3. Run your mouse over the metadata.db file. Click the little down-pointing triangle that appears, and select 'previous versions'
4. Select the version that is correct. It will be the newest largest version. You might also be able to tell from the timestamp, taking the one dated from before you added the new dropbox client.
5. Restore that version.
6. At this point, you have told dropbox which one is correct. This file will be downloaded to all the clients. However, on machines with the *wrong* db, the correct db will show up as a conflict file. Delete the wrong one and rename the right one to metadata.db.
An alternate way that avoids step 6 is to delete metadata.db* from every machine in step 1. If you do this, then step 3 must be modified to include clicking the 'show deleted files' button so that you will see the versions of metadata.db to select from.
Do not run calibre until all machines claim to be fully synced.
Good luck!
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