diff -up ntp-4.2.6p5/ntpd/ntp_timer.c.orphreftime ntp-4.2.6p5/ntpd/ntp_timer.c
--- ntp-4.2.6p5/ntpd/ntp_timer.c.orphreftime	2016-04-06 14:54:06.509912455 +0200
+++ ntp-4.2.6p5/ntpd/ntp_timer.c	2016-04-06 14:54:12.132926469 +0200
@@ -433,6 +433,7 @@ timer(void)
 		sys_offset = 0;
 		sys_rootdelay = 0;
 		sys_rootdisp = 0;
+		get_systime(&sys_reftime);
 	}
 
 	/*