Unsure of the command used I admit (not done by me), but yes, after the last reconcile / post we have duplicates reported in each of the editors' (3 of) versions when we run a command line check. We do have a command line repair tool ESRI alerted us to which fixes the problem. However, this requires all users to be disconnected from the system which has implications in our environment.
To perhaps make the situation more clear.
Editor 1 reconcile/post with admin version
Editor 2 reconcile/post with admin version
Editor 3 reconcile/post with admin version
Editor 2 reconcile with admin version
Editor 1 reconcile with admin version
This is to get all 3 editors versions the same.
Then....
Admin Reconcile / Post with SDE default.
Admin compress the database.
If editor1, 2 or 3 then tries to reconcile again....... duplicate primary Key is reported. This would - upon some research - appear to be a standard SQL duplicate primary key error.
Now.....
Load in the suspect dataset into arcmap.
open the attribute table.
What you find is that when you select one of the 'duplicated' features,the attribute table will report 2 selected features, I assume because there are two entries in the database using the same primary key. You can also try highlighting one feature from the attribute table and you will also get two features being reported as selected.
Anyone who's had this happen and can share info about it we'd like to hear from you. We are stumped.