I play my song and it sounds fine. Do this a few times. Then all of a sudden the violin or another instrument craps out, becomes inaudible.

Or I do my programming. Say up to C#5 from C5, works great. Next time it doesn't and next time it seems to trigger something on a different instrument.

 And then I crash, and spend 40 minutes loading on restart. Which works for a few minutes.

i7 960 slaves with 24gb ram and good video cards.

Off the top of my head, it sounds like you might have some program errors.  As has already been mentioned, having a keyswitch set in error can cause these kinds of problems, or inadvertently sending a wrong controller message (have done that from time to time-setting up a wrong controller that sends wrong messages for a given instrument).  For myself, I rely heavily on keyswitches, and have sometimes made mistakes when setting up a template.

On another level how are your MIDI tracks set up?  Some of your comments might indicate that instrument tracks are not set up correctly, and/or that some are set up to receive messages from multiple tracks.  These sort of error setups can cause all kinds of unusual results (from personal experience).

Overall, in terms of my own experience, when I am having VSL playback issues, or something has gone strange, I have accidently done something to create the error (one I've done more than once is to accidently set the metronome to sound on a certain instrument part).

Thanks everyone. I'm stalling right now because I'm in the midst of buying another computer to put Cubase on it and use this box as just a VSL slave.

So far, though, after deleting the channels that are going wonky (and re-adding them), the volume drop had gone away, thankfully. I'm still having issues with VEP5 jumping around all over the place though as soon as I add keyswitches into the Cubase track.

I have one VST3 instance of VEP5 in Cubase 6.5 on this computer. I also have 2 instances (EWSC and EW Stormdrum 2) from my slave, but that box isn't even turned on right now as I have to replace the OS drive, which is crashing (and causing the entire computer to crash when I hit play...again sporadically, but it also causes Cubase to crash on the master box...very frustrating...so I've removed it for now).

All of my channels of VSL samples go through VEP5 and VIP2, each on its own discrete channel. I should definitely check to make sure I haven't put two tracks on one channel or done anything else like that, butI'm pretty sure I haven't.

I think at the end of the day, other than the toasted hard drive on my EW slave, this is all going to turn out to be user error. It's all just too wonky to be something that's actually the software or hardware's fault lol.

Cubase should not be crashing-hopefully your new system will have at least 12 gigabytes of memory and two hard drives. If possible get a third solid state hard drive to load all of your programs onto. Sometimes deleting a midi channel that has gotten messed up is the only way to go rather than attempting to figure out what went wrong. I try to take notes on changes I make to a basic setup but don't always do that. It would be helpful.

Also, I am on a kick right now about using All Of The Training Videos for the software VSL makes available. Can't say enough about how many headaches I could have avoided if I had but gone through those first. Those will also help in finding ways to make your midi transcriptions come alive in ways you never thought possible. There is a lot of homework to using those ideas found there but well worth it in the long run. 

Cubase's manual is only good if you have already a well framed question to answer-otherwise trying to use it as a tutorial-Will Not Work. However, on Youtube, Steinberg does make available about a hundred training/tutorial style videos which are very helpful. Search for Cubase and Videos on Google.com and they will come up.

Have fun composing!