Postgres writes in to the log file the same date and time(server starts date and time) for all checkpoint operations. For other operations for example long queries or errors postgres writes in to the log current date and time.
>select version();
PostgreSQL 9.6.0 on x86_64-suse-linux-gnu, compiled by gcc (SUSE Linux) 4.3.4 [gcc-4_3-branch revision 152973], 64-bit
Try changing your log_line_prefix to log_line_prefix = '%p %u %m %e %i'
and reloading your postgresql.conf files (eg. pg_ctl reload)
I suspect the "%s" session timestamp is the problem, and you might be looking for the wall clock time instead (which is logged via "%m")
