I assume you've submitted the application from scratch, hoping you can get approved for the October test. If so, it's really somewhat of a 'crap shoot' with the NYSED. Right now they are very bogged down with getting the licenses issued for those (like myself) who passed the PE on April 13th. They appear to be weeks behind what they've done in the past, so maybe some folks there have retired. I work for NYS as well (but another agency) and the 'Tier 4' retirees are in full swing this year (those who started working for the State in the mid to late 80's), since they lose some Medial plan options if they leave after July 1st of this year. Hiring new staff is also an issue for the State due to the improve economy and the new 'Tier 6' retirement package is a far cry from what the State has offered in the past, so the only benefit a person gets now is some job security for a reduced pay scale.
In my case (waiting for my license), I tried reaching out to them (hoping for some State co-worker consideration), but they only take messages and their Email bounces back saying they have an unusually high volume taking place (you're guess is as good as mine on what that means - probably all of us waiting for our PE licenses annoying them).
I do have a suggestion for you on the application front however - keep at them. Last year they actually misplaced most of my application for about six months, including my Money Order payment. I did not find this out until I tried reaching out to them through Email to find out the status of my application. Fortunately I was still studying for the FE and did not need to schedule my PE exam at that time. When I finally got back an Email from that office (three weeks after I sent repeated Emails), and heard what had happened, I asked for one of the Supervisors to call me - of course mentioning I worked for another State agency. I did not get a phone call, but within two hours I got an Email back indicating that they found everything, and included an itemized list of what they had in my file. The Email also asked to let them know if there were any other forms I had submitted to experience references or with educational institutions, to which I replied 'No, none' - they did not respond back any further through Email, however I received a written PE exam authorization letter from them less than two weeks later indicating that I could sit for the PE whenever I chose to register for the test.
Well, I hope this somehow helped, but I really do feel your frustration. I am now concerned that unless I get my license number by the end of July, I may lose out of some cash as well since my employer pays an annual bonus to staff who have their PE, as long as I can prove I am fully 'Registered' by the cut-off date.
Good luck.