I am trying to migrate 2 collections from my configmgr 2007 r3 environment across to configmgr 2012 and am running into issues.

I have previously migrated collections that are at the root of my collection structure in 2007 r3 and now have moved onto collection at lower levels. The collections I am trying to migrate fit into the structure like this:

<Riddlesdown Collegiate - this is empty>
<Desktops - this is empty>
<S03-RM035 - this has clients in it>
<S07-RM037 - this has clients in it>

When creating the migration job I select 2 collections I want to migrate, untick the "migrate objects assiocated with the specified collections", choose the default security scope and the next until the end of the wizard. I leave the "transfer the organisational folder structure for objects from configmgr 2007 to the destination side" box ticked and run the job.

The jobs runs.

I've got a folder for "Riddlesdown Collegiate", a folder for "Desktops", 2 collections (S05-RM035 and S07-RM037) and 2 random clients that are not in the collections I have chosen to migrated. None of the clients that are in those 2 collections appear to have migrated across.

All the collections in 2007 r3 are populated using LDAP queries against AD, I have checked that the 2 random clients that have been migrated are not present in the OUs nor the collections.

If I migrate a collection that is at the root level, it migrates fine along with the clients in that respective collection.

Does anybody have any ideas?