Can you please elaborate on this configuration? What is the general nature of the configuration changes you're making? Or, how is your workflow affecting the product. I ask as I am in an organization right on the cusp of implementing JIRA, and I would love to steer the implementation team toward a more useful configuration than the clunky defaults, with which I've had prior experience.
* Setting up several statuses (more than in the default) to reflect backlog, selected, in progress, testing, deployed
* Creating an appropriate board which splits everything into columns by status and rows by user
* Setting up a few quick filters to find things like anything which has been in the backlog for more than 6 weeks or bugs which haven't seen activity in the last 48 hours
* Integrating GitHub. Being able to kick a ticket over to QA from your commit message is awesome.
Beyond that, I mostly focus on stripping out default things to make the workflow simpler. I don't need my software to enforce that I can't move a ticket to deployed straight from in progress, and stripping out those extra rules makes it easier to deal with.