Same. My instruments piano and trumpet are never-miss (though I hear the trumpet in Bb), and organs are more difficult for me too. I think organ overtones might be off pitch or something? just a wild guess.
Or, you could have a string stop pulled, which is purposefully slightly out-of-tune to produce a "string" sound when paired with an in-tune stop.
A typical "pipe organ" sound on a digital keyboard will often have mixtures and other mutations. I've found that settings with names like "church organ" tend to be purer, perhaps only some flutes and principals.