An easy fix would be:
record each Virus part individually! this way you have all the DSP power (that translates to the number of voices) available and therefore no note stealing.
Your problem seems to be just that: the Virus has a limited number of voices and DSP power. For complex patches, the number of voices can get high even with just one oscillator going (if using unison, for example); when it overloads, some voices won't be played at all 'cause there's no system resources left to reproduce them. Check the manual, you can set the priority of each channel, setting a channel to high priority means the system will preferably play this channel over others in the event of an overload.
Think of the multiple channels as something you use for composing, arranging and for previewing stuff only. Afterwards, record each part like you would with a Moog or a guitar. Slight change in workflow, but seems like you have no problem at all
cheers