After banging my head against the wall for many hours, I finally figured
out that .NET is adding escaped carriage returns, aka \r\n when the
queries are sent to HDInsight, which is causing the queries to fail. My code was loading the queries from files on disk like this:

string query = string.Empty;
using (var fs = new StreamReader("CreateTempTable.hql"))
{
    query = fs.ReadToEnd();
}

I figured this out by looking at userArgs
file in the templeton-hadoop directory to see what the jobs looked
like, and they appear like this:

"ADD JAR wasb:///user/jars/csv-serde-1.1.2-0.11.0-all.jar;
\r\nDROP TABLE IF EXISTS temp;\r\nCREATE EXTERNAL TABLE temp
(viewerId string, asset string, device_os string, country string, state 
string, city string, asn string, isp string, start_time_unix_time bigint,
startup_time_ms int) \r\nROW FORMAT serde 'com.bizo.hive.serde.csv.CSVSerde'
\r\nSTORED AS TEXTFILE LOCATION 'wasb:///temptable';\r\n\r\n               "

As you can see, the query is littered with escaped characters which causes the HIVE query to fail.
These same queries can be submitted via PowerShell no problem.

So, basically, I removed all the linebreaks in Notepad for my HQL and everything worked.