Yeah – out of 814k DPS that’s only a 0.36% DPS difference, it would be extremely difficult to get any closer than that with consistency in an optimizer.
You want to think of it as a tradeoff between speed and accuracy.
The most accurate way to figure out the best setup would be to go in-game and try them out enough times to average out the game’s inherent randomness (crits, procs, etc.). But that is more or less impossible… it would take until the end of the universe in real game time, and chances are you would get an upgrade or two before finishing, making it moot anyway 
The next most accurate way we have come up with is simulation. That’s pretty good – for a given setup, it can get a pretty accurate answer in about 5 seconds, give or take. But when it comes to best in bags… there can be upwards of a trillion combinations worth trying if you have a lot of good gear. To simulate all of those we’re back to around 100,000 years (actual estimate, not made up)… once again, not that useful.
So we create “gearing strategies” which are predictive models based on a small sample of simulation data. They lose accuracy (we are in the process of reducing and actually measuring how much accuracy is lost, but it’s around 1-2% right now), but they can get an accurate answer for any given set of gear almost instantly. But even then, it would take a long time to do a trillion combinations… maybe around 10 minutes, because it’s only almost instant. That’s a long time to wait when you press the “best-in-bags” button, not to mention how expensive it would be to run – we’d have to charge you ridiculous prices to host that.
So the final piece is our combination optimizer. It knows how to sort through all those combinations intelligently and find the best one without actually having to test all of them. You lose a very small amount of accuracy from this, it is actually no loss in over 95% of cases, and less than 0.25% for the rest. But now you can do best-in-bags in under 1 second for most cases.
So to go from 100,000 years via simulation down to 1 second via best-in-bags, you end up losing around 1-2% accuracy right now, and we’re always working on improving that. Our ultimate goal is to always be within 1% of the best simulated setup for your character, though most of the time it will be much closer than that. We feel that is the practical “floor” for accuracy, and we are closing in on reaching it. Anything lower would be prohibitively expensive to build, and also of dubious usefulness to even the best players (for reasons that I plan to write up sometime soon).
That all said – we created the simulator for a reason! If you are able to find a setup that is better than what best-in-bags suggests, by all means use it. We plan to actually make that easier in the near future – if you want to let your CPU crank away and try to refine best-in-bags further than what the optimizer can do, we’ll give you a way to save and use those results with ease.