If the second virtual instrument is out of tune compared to the first then one of the instruments might accidentally be transposed. I suppose this could happen within the instrument plug-in itself -- many virtual instruments have a tuning or transposition setting -- or I guess there could be a transpose value enabled in the track parameters [on the left] for one of the instrument tracks..? I'm not a Cubase user and I don't have access to any version of Cubase [Cubase 5 seems to be a really old version of Cubase], so without being able to poke around in your session I can't offer you any more specific advice, other than to look at both instrument plug-ins' settings [within the instrument plug-in windows] and the parameters for each instrument track, to see if there's an accidental transposition dialed up somewhere..
If you can't find any transposition settings that are causing the instruments to be tuned differently then I guess you could try a few tests..
- reload both instrument plug-ins and see if they then play in tune, or
- make two new tracks and load the same two instruments on the new tracks and see if the new tracks play in tune, or
- create a new session and load the same two instruments into that new session and see if they play in tune there..