Thanks for the vote of confidence!
Just be clear on my setup, while my understanding is that Active Directory (Windows server) handles the authentication and is the basis of the file server containing the network based home directories / storage, I can't guarantee Open Directory (OS X server) isn't involved as the OD server is bound to the AD server and ALL clients are bound to BOTH AD AND OD.
The theory (and we all know how that works in practice!) is that this means AD handles most things and OD handles the managed profiles on Macs (Like AD handles group policy for Windows clients)
in answer to some questions:
Yes, I have rebooted, and still without pop ups. That clicking restart or by clicking shutdown and the powering back on after the auto power off.
I specify that the local home directories are stored on a non-boot volumes for ease of back ups and restorations. This means that when creating the mobile accounts through the GUI, they are created as "external users" , this means that the user only appeared in the User & Groups preference pane when logged in. The option used creating via terminal meant they are added as "mobile users" and continually appear in the preference pane. A small difference, but maybe relevant.
Best of luck all