The previous model, X100, black version used to be sold as limited edition with all the black accessories included not sold in the retail shop then (black hood, filter, premium leather case, etc) with a serial number card indicating the limited number produced.
Was asking for more than $2000 for the full set, and sold like hot cakes then (as compared to the silver X100, at around $1600).
You can still find the X100 Limited Edition Black now at some reputable stores at Funan, brand new set sold at around $10xx. Half the price of the initial selling price.
Guess Fuji realised that they cannot do the same for X100S, as the "limited" edition does not really maintain value or appreciate in value like the Leica cameras.
Good that they are selling both black and silver X100S models now both at the same RRP, but as what most buyers are aware, black ones are either less in stocks, or more highly demanded (both due to the X100 black limited edition impression, as well as black being more discreet and sexy), thus retailers will probably be selling this at RRP or near RRP, while they are willing to lower the price a little for the silver X100S which is slightly harder to push.
Ironically, when I bought my Leica M9P Chrome with the Chrome 50lux, it is chrome silver version that it very rare and limited, and black ones normally sell at a slight discount as compared. Probably some differences though, as the black paint of Leica cameras tend to "brass" more easily and the chrome set maintain its exterior look better.