I am experiencing the same issue with my study permit extension!! I have done 5+ applications on the portal so far and it is the first time I did not get the confirmation message/number right after the payment. Panicking!
It has been a while but may I ask - did you get approved the second time you applied it? I came across the same issue. I am 100% sure I submitted the letter of enrollment but they said I had not provided it: (