Asset Server works for scripting files the scene file it never changes/updates.

When we commit our changes in unity iPhone then update from the server the scene data never gets saved. So if we create a Game object then save it then commit the changes they never appear when you try and update from another computer. Any help resolving this would be massively helpful.

Is it happening with the scene file you currently have open? If so, try switching to another scene (and answer yes if/when it prompts you to save that scene) before committing the scene file.

Unity iPhone doesn't have the feature that Unity 2.6 does, where it notifies you that the scene changed when you update from asset server. Be sure to reload the scene whenever you do an update with asset server to make sure you have the latest version loaded.