Maya,
I have 4.0.4536 installed on all machines. slaves run on OS 10.6.1; master runs 10.5.8. Kontakt is version 3.5.025.
It's seems to be an intermittend bug. It remember it to happen like this: fresh reboot of all MAcs - load template, things run fine for a while; closed Logic project - opened same template - some Kontakt channels won't play any more. I did try it with a new Logic project to rule out an error in my template, but encountered the same problem (but the bug might have already been in the system by then). And I think it happened when I left the VE PROs connected.
I'll try to determine the steps to reproduce it as soon as my schedule permits.