I have 10m and I don't have this issue...
I don't think it coming from nginx.
There is very few parameters in nginx config that could explain your latency...
Does it happen only on reboot of VM, or it happen when you restart nginx, or uwsgi. What happen if you restart nginx only vs restart uwsgi only. And what happen if you try to start manually uwsgi after reboot of the VM before first aptempt to connect to your app. Maybe uwsgi is not started and get strat by nginx, that should not be the case though, they have both to be strated independently.
You can try your app in other VM and determine if the latency was there or not.
All these test can help you figure out where to dig up further.