Hi Danny,
Barring disasters, I operate a set up that includes one master and three slaves (though I only need all if it's a big orchestral cue with choir and sound design). However, as I already said, I get the problem just running the master PC on its own.
VEP 5 and Kontakt 5 don't seem to play quite so nice together as the version 4s did. They have both made some architecture changes which, as the issue with Kontakt reloading samples when you first selected tracks demonstrated, these have introduced the potential for new conflicts. Of course, as I understand it, you have been having these issues since before those versions were released.
Since Cubase 7 I also have Kontakt issues where instruments spontaneously transpose without showing any settings changes, in Cubase 6 - that used to spontaneously transpose even when the transpose insert wasn't active. And all versions randomly zero the main volume on Kontakt instruments unless you set them to ignore incoming volume & pan messages.
Having said all that, I wouldn't be at all surprised to find that the culprit was Windows! ;-)