I've also been encountering this issue. My configuration is:
Platform: OSX
Postgres 9.6.1
PostGIS: 2.3

Relevant dependencies:
hibernate-core/entity-manager/spatial: 5.2.7.Final
postgres (org.postgresql): 9.4.1212.jre7

Using com.vividsolutions.jts.geom.Point with an @Column annotation. The database column is of type geometry(Point,4326)

{{org.postgresql.util.PSQLException: ERROR: Invalid endian flag value encountered.
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)...}}

I poked around a bit and expected that JTSGeometryJavaTypeDescriptor would be used to wrap/unwrap the values but it is not being invoked. I understand a proper test case is probably required to solve this and I will try to put one together. I wanted to at least document what I've found so far.