What specific version and build are you seeing this error?
When I run a test with a table that has all its columns part of the primary key, the sync works on 16.0.0.2018 so it is working in more recent software. Here is a log snipet for the test:
I. 2014-11-06 10:45:51. <1> upload_insert t
/* Insert the row into the consolidated database. */
INSERT INTO "DBA"."t" ( "pkc1", "pkc2" )
VALUES ( {ml r."pkc1"}, {ml r."pkc2"} )
I. 2014-11-06 10:45:51. <1> upload_update t
/* Update the row in the consolidated database. */
/* No columns to update. */
I. 2014-11-06 10:45:51. <Main> System event on shared administrative connection: