have you tried playing with the PHASE INIT knob? Perhaps there is an issue with the OSC starting at different parts in its waveform with each key press which would sound like it is out of tune? Have you checked to see if any LFO assignments are present either in the dedicated LFO page, or the MOD Matrix? The fact that you say some patches are in tune while others 'appear' not to be would mean these patches that sound out of tune may have modulation of some sort going on that you aren't aware of. Any time I had ever had an issue like this resetting the Virus would fix it. If there was a real problem, I would think the entire synth as a whole would be out of tune, not just some of the patches.
Good luck however!
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