I think that you should start by having a look at your Scheduled Tasks and verify that there is no Inventory task set up for computers in your domain. Those inventories go to AD and pull all of the computer accounts (dead or alive) and add them to the task scope. All of these accounts, in turn, get added to the Managed Computers View. I suspect this is the issue.
If possible, you can narrow down your inventory tasks to just machines in a particular OU(s) that have the machines you want to collect information on.
Finally, it's worth mentioning that in the next release (005), we will be introducing some new computer management rules to help filter out the dead machine accounts.
Hope this helps,
Thanks, this was exactly what I was looking for.