I've got a Python script that reconcile/posts edits from child versions to Default. If a version is created by the admin account, it will reconcile just fine. But, if a version is created by a user, we get conflicts when running the geoprocessing tool through ArcPy. If I do reconcile via ArcMap, there are no conflicts. It doesn't matter if the version has just been created, with no edits made to it.
Strangely, any user-created versions that are reconciled against an Admin-created version, will reconcile just fine. It's only those user-created versions that are created directly from Default.
I didn't have a problem reconciling between Public versions, but I got the same error when reconciling up to a Protected version. I got around this by inserting the owner information before the version name (ie, 'owner.version' rather than 'version'), and when logged in as SDE the script ran fine. Russel is correct that the wrong error message is given - luckily this is one of the first threads I came upon.