I also have a lower hash rate with the new version than the old one.
Old one : 642
New one : 620
Using it on Windows 10 64 Bit 1703 and 385.69 driver version.
dropky released a new version to address this issue:
https://github.com/nicehash/excavator/releases/tag/v1.3.2a- equihash bug fixes & improvements
Added M (mode) parameter for equihash.
Use one worker per device when running with M=1, otherwise use two workers per device.
I will upload Debian packages for Ubuntu shortly.