Not sure if anyone else has run into the same issue, but it appear that mandatory profiles are not compatible with the new Windows 8 Modern Apps. As soon as the profile is made mandatory, the tiles for the apps no longer appear on the start screen. Non-Modern apps that are pinned (using the sysprep/audit-mode method) are still visible however.

Just a heads-up really - we're getting around it to a certain extent by reluctantly giving people their own profiles rather than mandatory ones, having already customised the default domain profile so they'll at least start with a good set of icons on their start screens.