When upgrading to 1Password version 2.5, we have have several reports from .Mac members that the new 1Password keychain has all of its contents duplicated. For instance, a 1Passwd keychain from version 2.4 containing 400 items would end up having 800 items, or even 1200 items in the new 1Password keychain in version 2.5.
This issue is being caused by how .Mac is performing the sync process. From what we can tell, there are two causes of the duplication.
Known Causes of Duplication
The first cause of duplication is running the Migration Assistant twice. You should only do the 1Password 2.4 -> 2.5 migration once on a single machine. If you migrate on two machines, they will each sync with .Mac and create duplicate entries. This is because each item is assigned a unique name when it is created, so it is technically a new item as far as .Mac is concerned.
The second cause seems to be a timing issue with the .Mac servers. One user mentioned that it took over 7 minutes for his synced keychain to appear on the .Mac servers. It seems that during this delay, the .Mac syncing happened again and thereby created the duplicates.
Fixing a Duplicated Keychain
The best way to fix the duplication is to migrate the data again. All your original data is still available in the 1Passwd.keychain file. Here is how I would recommend proceeding.
First, turn off .Mac syncing on all your machines. You can then rename the new 1Password keychain on each machine. I never recommend deleting keychain files, so rename it to something like 1Password.keychain_duplicated. Here is the file to rename:
/Users/your-user-id/Library/Keychains/1Password.keychain
Notice the spelling, 1Passw*OR*d.
Now you can start 1Password and go through the Migration Assistant. Once done, replace the .Mac copy of your keychain with your new local one. The process for doing this is detailed in dotMac Syncing Howto: Forcing Keychains to Sync.
Once the syncing is done, wait 20 minutes to make sure the .Mac servers are updated. Now on your second machine, rename the 1Password keychain, and then replace the keychains on your Mac with the ones from .Mac (the opposite of the steps in the above article).
Be sure not to enable automatic .Mac syncing until you get this resolved.