We are using the tblproperties ("skip.header.line.count"="1") when creating an external table.
When we do a select * from table we get it back as expected without the header present in the result set.
However when we do for instance a count(1) we get the header back in this count (tested with a select * from table and paste it in notepad to find the amount of rows)
If we also do this with a select distinct(column) from table we also get the header as a distinct value.
I cannot show the exact statement because of NDA so i changed those values to test.
I can also tell you it is not just at our HDInsight but also at another company we are working for. It does not Mather what is in the data as well. so for testing purposes: