One other factor in the perceived latency of playing Box Of Stops is the choice of instruments on the [[Stop|Stops]] in your [[Registration]].
Ideally you are looking for instruments with a short [https://en.wikipedia.org/wiki/Synthesizer#Attack_Decay_Sustain_Release_.28ADSR.29_envelope attack phase] - how long the sound takes to reach go from zero to its peak level.
A classic example of an instrument with a slow attack phase is the Pan Pipes, with the lovely breathy start to each note. However mixed in with other instruments with a quicker attack phase, the overall effect will sound quite 'raggedy'.