What about the Deleted field? Did any computers/servers show a 1 in that field? If yes, those computers/servers won't appear in the console.
For those computers that are showing as duplicate hardware IDs, follow the kb for deleting the registry key and check both to ensure their hardware keys get re-created, and are different on each one. Then, check to see if they appear in SEPM.
Had to restore an older v11 database to find out what went wrong with the query. Seems they changed things around in v12.1... Imagine that.
Try this query to check Policy Mode for those servers (Again, change [databasename] to reflect your database):
SELECT [CLIENT_ID], [DOMAIN_ID], [GROUP_ID], [POLICY_MODE], [COMPUTER_ID], [HARDWARE_KEY], [COMPUTER_NAME], [COMPUTER_DOMAIN_NAME], [USER_NAME]
FROM [databasename].[dbo].[SEM_CLIENT]
In this query is the group_id. For those computers that have duplicate names or duplicate hardware ids, do any of them appear in those groups? To find the correct group, you'll have to find another computer where you know the group it is in and check there.
One other thing to check - are you using the Java console or web console? If using the Java console, are you using the version of Java compatible with SEPM v11? If using the web console, are you using the version of IE that is compatible with SEPM v11? I have had issues before when I upgraded my Java or browser. I wouldn't think it would cause this issue, but you never know. A good Win32/Win64 app would be greatly appreciated.
Along those lines, you might try deleting your Java and browser caches to see if you get the same results.