I found a post logstash-6.7.0 failing to start that suggested the content of classpath environment variable could be at fault.
I temporarily set classpath to "" in the command line window before running the ncv.conf file that uses jdbc to connect to the database and that saw logstash running fine with data returned. I have no idea why that is and what in classpath was causing the issue but this is what my classpath looks like before blanking it
C:\Program Files (x86)\IBM\WebSphere MQ\Java\lib\com.ibm.mqjms.jar;C:\Program Files (x86)\IBM\WebSphere MQ\Java\lib\com.ibm.mq.jar;e:\app\ojdbc\;e:\app\ojdbc\ojdbc6_g.jar;e:\tika-app-1.20.jar;.