After some run around I have a couple updates to this issue for those who may be interested. 

I spoke with tech support on the phone and was instructed to call NY DTF and see if they had any information on the scheduled payments. Took me a little while to get a POA signed but I finally did, and NY had no info aside from the payment already made. 

Circled back with support and did a remote session. I was told the issue was that the scheduled payment date falls on a holiday, so the payment did not get made. He then had me re-enter and send the Q2 payment with a prospective date and it seems to have gone thru fine (don't have ack yet but fingers crossed). 

I accepted this uncritically at the time, but after reflecting there seem to be 2 problems with this. 

1 I am not aware of any recognized holiday falling on June 15, if I am missing something please let me know. 

2 The default payment dates are the deadline for each quarter. Why the hell would the government set the deadline for a holiday? And if they did by accident, wouldn't there be some sort of memo about it somewhere? I can't find anything. 

Further, I was under the impression that these payments can't be made or altered in any way after the return is filed, but somehow we went and filed the payment 2 months later with no issues. Can someone enlighten me? I am so confused.