Try setting the Kontakt plug-in to save minimal undo states:
https://forum.cockos.com/showthread.php?t=72349
Also if it worked OK before, maybe you added more instruments/plug-ins (and sample libraries!) to the plug-in folder later? This could increase seek times, it's generally advisable to have sample libraries (or anything else that consists of many files) in a folder that's not part of the plug-in search path.