OK the S2 now has been running for 16hrs and the (avg) has dropped down to 903gh/s. I've emailed Bitmain about getting a replacement but haven't heard back yet. Has anyone had any experience with Bitmain when it comes to warranty issues, or how supportive they are in resolving these types of issues?
Are you sure all blades working well?
As tzortz said above, are you sure all blades are working well? Do you see green lights flashing on all of them?
You might just have a faulty board or 2. Try by taking them out: take one out, boot up and see if it runs at 900 Gh/s or 800Gh/s. If it runs at 800, then put that board back in and take out another one and try again... that way you can narrow it down to which boards are faulty and send those ones instead of sending the whole machine... that way you can still mine at 800-900 Gh/s while you wait.
I emailed Bitmain about my faulty machine, it took 2 days to reply, but they sent all the necessary details to RMA, with postage at their cost.