My guess: very minor rounding issue. 1 point difference basically means that it is an equivalent solution.
For the record, we are very close to releasing a beta of a new optimizer that absolutely guarantees the highest-scoring solution in most cases. The current site runs a very good approximation algorithm that often gets optimal, but can't guarantee it.
For the profile that you linked and your custom weights, the approximation seems to be having some trouble... not sure why. I ran it through our new optimizer, and the following is the best possible solution: *(* that is... if the new optimizer doesn't have a bug, which is why we're doing a beta of it first! But so far I haven't been able to beat this score.)http://www.askmrrobot.com/wow/gear/e8d41cd4-7ead-451f-ac6b-93a670c8084f
Note that I locked in the optimal gem setup, then the current optimizer is properly picking the reforges and enchants to go with it. This goes over your haste cap slightly, but that just happens to be the combination that scores highest for your weights (~1100 points higher than your current setup, or about 1% better).
This beta will be available in the next couple of days hopefully... keep an eye out for an announcement, it will be a public beta that you can use directly through the main website by turning on/off an option to switch to the new optimizer.