I have headless running on linux with the new update, addresses are generated properly and I can withdraw from coinexchange.

Don't use the master branch on github, instead use the src package download from here:

https://github.com/equitrader/Equitrader/raw/6c30d895bcaafd1413f23424730bde1a48414edf/equitrader-src.zip

This one compiles out of the box without having to hack the source, and the resulting binary is called EquiTraderd.