Here’s what I think is happening. Since the DraftEventPlugin starts its execution before the Shotgun Plugin, the Shotgun Version has not been created yet so that’s why you are getting:
WARNING: Could not find an associated Shotgun Version ID. The Draft output will not be uploaded to Shotgun.
Note that your Shotgun version will effectively be created, but just a bit too late. If you requeue your Nuke job (by right clicking on it from the Monitor and selecting Requeue Job – no need to submit your Nuke job again) Draft will be able to find the Shotgun version and your shot will get uploaded to Shotgun.
On the other hand, if you set Create Version on Submission to True in Tools->Configure Events->Shotgun, I believe the Shotgun Version will be created right away and Draft will be able to find it when it needs it. I tested this locally on my machine and it appears to work fine. (Note that I had to restart the monitor and the slave after setting that option to make this work.)
I’m very sorry you are experiencing that issue. I hope we’ll be able to make this work for you quickly!