I have the last version of grafana and Elasticsearch version 5.6.9 here.
With the graph panel and auto interval, no lines are drawn at an ES template refresh interval of 10s if the time window is equal to or less than the last hour. Bars and Points are displayed only lines have this problems. If i use an interval 10s instead of autointerval, the lines are also drawn. I do not have this problem with a ES templates with refreshinterval of 5s, here works autoinerval for lines correctly.