Phew, I've read the question about three times and still can't understand it.
AFAIK, pretty much every 'tuned' patch made should ideally reference to a base semitone value of 0, or transposed an octave or two above and below, as Juho pointed out. When you've learn theory and stuff, then the 7ths, triads etc. come into it. And of course for the non-tuned instruments (percussion, sfx, etc.), anything goes.
And that's pretty much standard across all synths.
Actually, have you got one synth globally tuned to a different key than the other?
If one synth is globally transposed, say, 4 semitones up from another, second synth, then yeah, you're going to have some serious probs tuning patches to sit well between both synths.
Best set equal global transpose settings for each/all synths at any one time.
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