Yo, I feel for ya mate.
It is pretty much a known issue with the Virus Rack Classic/B that the knobs on that sucker are stuffed. (see below posts on this forum)
http://www.sunesha.nu/virusforum/viewtopic.php?t=1643
Post your problem and dissatisfaction there and Access might take notice one of these days...
Access know about this problem, but aint really gonna do nothing about it, it seems that the way the Rack OS interprets the kob movement on the relative knob encoders is wack... It gets confussed. Which maybe related to your Cubase issue.
Firstly make sure you disable any Midi LOOP problems when your writing values in the controller lane, Just pull the MIDI out cable out of the back of the virus so it doesnt send any data back into cubase and cause problems. If this fixes it. Then you can set up MIDI filters in Cubase to filter any CC or SYSEX events coming in from your virus.
That said, what version of CUBASE are you using. The original SX v1 had major problems and you have to do a MIDI PORT FILTER hack to get it to work proper...!!!
Good Luck, I would suggest getting an external MIDI controller to control the settings on your RACK, It sucks that you pay all that money to get something you think should work... BUT, thats the way the cookie crumbles....