When I made my application for my spousal visa a week ago Friday, it was being temperamental about accepting my payment for the application. Basically, it said that my payment *might* have gone through, but there was a chance it didn't so I should wait 30 minutes to see if I got a confirmation that my payment was received, and if not to try again, and if that did not work, to call the consulate directly to make arrangements for payment (since you can't get your biometrics until your payment has gone through). Thankfully I got my payment to go through, but they are aware of the problem, even if they'd fixed it.
Also, when filling out my e-app, there were certain boxes that although I filled them in, could not get them to appear in the final thing to print out for the life of me, so I'll have to write that info in by hand.
Sorry I don't have any answers either, but there do seem to be a lot of gremlins in their system lately.