I recently ran into an issue whereby Storyboard changes were being lost when switching from Storyboard/XCode->Xamarin Studio. Some time earlier, I had set the date back via Preferences a couple of days in order to do some iOS testing. On a hunch, I changed the preferences to automatically set the Date - and I observed that changes were no longer being lost! My take is that Xamarin Studio must be caching certain files (IE Storyboard, outlet source files, etc.) and relying on timestamps to determine whether to update or rollback the changed files?
If this is a known issue, I would wonder if this strategy could be modified since adjusting the Date is a very common technique to test iOS?