Jpayne,
We've had a couple of other reports of intermittent/occasional issues on El Capitan. We are currently investigating. Would you be willing to email a Pulse Log bundle to "
[email protected]"? If so, I'll make sure the proper developers take a look. Alternatively, your IT administrator could reach out to our support organization at http://www.pulsesecure.net/support and create a formal tracking ticket.