COVID-19 delayed my debugging of this enough for the thread to lock, wanted to post what ended up making this work.
The suggested TPS60400 doesn't supply enough current for my application so I was determined to get this LM2776 to work.
From experiments we found out that a small resistance (4ohms, likely less will work as well) was enough to get the device to startup properly every time, I considered using a reed relay to power this up with a 4ohm resistor on the Vin then short the 4ohm resistor once the device was running to eliminate the voltage drop. This may have worked but another work around I stumbled across was using a longer wire to power the entire project also fixed the issue. using a longer wire allowed me to keep the current PCB design and is cheaper than the added resistor switching complexity so thats what I went with.
TL;DR switched from a 3ft USB cable to a 15ft USB cable, works fine now.
