@tywyn the largest difference is that SYSTEM is not allowed (by design) any interaction with the user or userspace at all. This probably also means the user’s account too. This is Microsoft’s design, not ours - and they went that route for security reasons.
When developing snapins, if your snapin will work manually but not as a fog snapin (and you’re sure you deployed the snapin correctly), you can normally assume the problem is because of the above.
Try what @Avaryan posted.