Are you saying that the played notes does'nt have latency, but only the modulation?
If the notes have latency, then please tell which driver you use, and if it's the same driver, soundcard and soundcard settings you use with your other applications.
Are you in standalone mode or using the application as a plugin in a host?
Arturias Prophet application is both a Prophet 5 and a Prophet VS. Some sounds even use both in the 5VS setting. Which cutoff has you assigned to? And which preset do you use?