Try accessing the Funnelback Public UI directly for the funnelback_documentation collection (without Matrix involved), perform some queries and clicks, and examine the corresponding output in these log files.
It's also possible that:
you're using a template that doesn't refer to the click tracking URLs in the response data model (transaction.response.resultPacket.results.clickTrackingUrl), or
the click tracking URL prefix has been incorrectly configured, or
there has been some additional reporting blacklisting configured.
If you're wrapping the Funnelback response in a Matrix page requested on a user's behalf, you will also want to ensure you're passing through the remote user's IP address for accurate logging.
Thanks for you reply gordongrace, followed your advice and found the following:
If I perform some queries and clicks directly in Funnelback Public UI, then update the collections Analytics, I get a new Archived log file that contains the new query and click data.
But when I search within the Matrix site, then hit update analytics, I don't see that a new log file is created. The system is set up to update analytics automatically daily and creates a new Archived log file which gathers query result but for some reason not click data. I'm contacting my system admin to see if I can better understand the setup, but seems like a big loss not to be able to collect click data.