I am having the same problem with the "our records indicate the following items are still missing" with nothing marked as missing in the table below. I sent in an email on Friday (should've done it earlier in the week but it didn't occur to me), and got a response this morning.
They said my file has been forwarded to the committee for review, and that the new system still has a couple bugs. I just logged in to check my application and the blue box that says "Your file has been forwarded to the Graduate Committee for review" just appeared this morning. So, if you are having a similar problem and you don't see the notice that says your file has been forwarded, it doesn't hurt to contact them, I suppose. Better safe than sorry when it's a technical issue.