Roland --
If I'm not mistaken, the reverb from parts 2-16 are applied through part 1. I'm not sure if the send volumes are affected by the part volumes themselves, but this could definitely be doing things with your reverb/delay to some degree either way.
At first, I was a bit put off by this as you likely are. I would go through banks in Single mode and save them to a 'favorites' bank, and they would just never sound the same when I wanted to use them for a track. Soon I accepted that I couldn't have them all sounding the same. I just learned to work around this limitation though. I like the sound of the Virus reverb(particularly the Reverb+Feedback algorithms) to give a sense of space, but it's not my go-to reverb, so I've started applying many of my effects in-the-box. I'll tend to use the virus reverb for swells and over-the-top reverb rather than for subtle ambience, though it can do that too. When I work in multi mode I'll usually turn down the reverb for every patch and then dial back an amount that sounds like 'enough' for me to move on to other things. (If I know it's there, I'll leave it till I'm finished more important details.)
Other quirks of my workflow: When in multi mode, I don't use stereo outputs unless I need to(for things like pads or fx) which gives me more outputs to use and thus more routing options with plugins in Live/Logic, where I can insert or bus out to plugin reverb/delay/compression etc. I may layer patches in my Multi too, as the Virus sounds great when layering patches: If you haven't tried this, do it! Sometimes when I want stereo I'll create slightly different versions of the same patch and send them to different mono outputs, and them pan them differently in the stereo field, group them in Logic and add modulation effects, etc. This uses more voices than Virus stereo but it offers more interesting possibilities for the additional voice/cpu cost.
In my experience(which, I should say, isn't *that* extensive but it's all that I have) the sound that you described is the sound of an analog synth without effects. They sound harsh, dry, buzzy and raw. The Virus sounds better than most in this regard, but it still has a harshness to it before you apply effects. The more you use it, the more you'll learn how to make it sound the way you want. Video tutorials are helpful, like this one from Kamui :
http://www.youtube.com/watch?v=lIUluK8OFNM