The JSB's tend to have softer lead skirts -- accuracy improves if you make sure the skirts aren't dinged or bent and if you use a pellet seat tool to consistently seat the pellet in the breech. JSB's also tend to vary more in weight from pellet to pellet. The FTS seem to be a harder lead alloy with less fragile skirts and are much more consistent in weight.
In general, I have found that if I weigh the JSB pellets and sort them by weight, and then take care seat them carefully, they will out-shoot most other pellet types in any of my air rifles, but if you just load with your fingers straight out of the tin, the FTS are hard to beat for consistency.