I have a similar problem with Kontakt2.1.1.001 in FLStudio6.0.8 and the VSL Horizon samples. The best it works for me, if I turn on "Fixed Size Buffers" while playing it realtime in FLStudio, but turn it OFF before rendering (if it's checked while rendering the instruments seem to swing around the clock). "Rendering Mode Notify" should be also checked (otherwise I get the same problem with some silent places).
Wow, this is really a masterpiece !!! Really one of the best remixes here. More of such things.