have you tried the tracking data also with the ARMediaToolset app?
Anyway, we are aware of a bug related to the Unity plugin, and I suspect you are having troubles exactly for that bug. Specifically in order to use the 3D tracking features on iOS you'd need to first generate the cache for the actual tracking configuration otherwise the tracker won't even start.
To generate the cache you need to:
1) open the conf.xml using a text editor
2) modify the following entries:
3) copy all the tracking data (images, pointcloud and modified conf.xml) into the ARMediaToolset app and try the tracking there, first of all tracking should now work, then the cache file (with extension .flann) will be generated
4) copy that cache file and the updated conf.xml file back into your Unity project, now tracking should work also with the app built from Unity.
Hope this helps.