If anyone is experiencing the payment processing issues Stanford is dealing with, do not fret. I spoke with them they will have record of the submission and sort out payment later.
I went on the admissions page and sent in a help email and received this auto response, it couldn't hurt to do the same so you have a record:
"If you are notifying us about your Round 1 application payment issues, we are aware of the problem and hope to have them resolved soon. We are not able to respond to each help request. Please don’t submit with the pay by check option. We will notify you when the issues are resolved."