calico
what's happened to me is that the textures appear with the correct path in the multishader, but just don't render. I put this down to them being in different places. Sometimes I'm too lazy to import and re-assign all the textures to the same directory, and this incarnation of TG2 doesn't seem to like being asked to look in more than one place at a time for it's imports, so re-assigning (to where they already are) in the multishader seems to remind it.
I understand what Treddie is saying, Sometimes these glitches repeat, sometimes they don't. I 'think' it has to do with the memory usage. You tend to get less glitches early on in a piece of work, or when you've just saved a file, than when you've been working on it a while - and if that's true, I'm not even sure you can point the finger at TG2, I'm running Windows XP, and that does so much stuff behind the scenes that we never asked it to do, don't really want it to do, and (speaking personally) can't seem to stop it doing, that it seems to screw up 'simple' programs, let alone the really memory intensive ones.