That isn't a Hot Standby problem, a recovery problem nor is it certain its a PostgreSQL problem.
Do you have any theories on this that I could help investigate? It happens even when using pg_basebackup and it persists until another sync is performed, so the files must be in some state that that it can't recover from....without understanding the internals just viewing from an outside perspective, I don't really see how this could not be a PostgreSQL problem....