I am having the same issue.  I was sent a invoice through QB and went to pay with a check and it is giving me the same message  (Your payment method was declined. Please use another method or try again.)  

I have never had a issue paying my invoice on QB. When the person that sent me the invoice called and spoke with QB, two times today, they are telling him they don't see anything on their end causing the problem.  I then called and spoke with my bank and they do not show declining any payments in my bank account.  When will this problem be fixed???