Hi Steve - I fought with this problem recently for an Elasticsearch java client. I found it best in our case to pass the location for the log4j.properties as a java property. Also, some OS's differ and require "file:" as a prefix to the location.
Example:
-Dlog4j.configuration=file:%ESHOME%/config/log4j.properties
I didn't notice this same error for the server, neither for the .zip install or an RPM install.