I have my persistence.xml with the same name using TopLink under the META-INF directory. Then, I have my code calling it with:
persistence.xml
TopLink
META-INF
Try also copying the persistence.xml manually to the folder \bin\META-INF. This fixed the problem in Eclipse Neon with EclipseLink 2.5.2 using a simple plug-in project.
\bin\META-INF
EclipseLink 2.5.2