When you registered your layers as versioned, did you select the "move edits to base" option? It seems like I have seen problems when this option was selected. If it is easy to test, maybe try changing this setting one way or the other. Sorry for being vague - this is all I remember.
Are you looking at the featureServer service on both the iOS and the Windows device? As opposed to MapServer on one device and featureServer on the other?
Do the changes from the Trimble Juno show up if you put the featureServer service in an ArcGIS Explorer Online map? This might tell us if we have an issue on the client side or server side.
Best wishes,
Paul Lohr