Yes - I've had the same behavior: I can load up a number of channels on-by-one and they seem to work sometimes but then won't work at all when I re-load the saved project.
I now recall that I went down a similar path many weeks ago when I first started debugging this problem. But I got sidetracked into trying to match VSL's hardware setup... I guess it's time to revisit it.
I'm willing to bet all your MIDI channels will work so long as your total sample usage stays below 3 GB. That's my experience. I can get all MIDI ports/channels to work as long as I stay under the 3 GB limit.
So maybe it's a combination of the 3 GB limit and the total number of channels being used.
But it doesn't seem possible - I've seen posts from people using 7+ GB of samples. Surely they must be using more than 13 MIDI channels, right?
I'll do some more testing today and see what I can come up with.
rgames