Theoretically it's of course possible that it's not detecting scenechanges correctly, however a few missed or a few added keyframe won't make a big deal. The default works very well for everyone. If however it is missing a lot you should decrease the threshold by 10% or so, if it adds a lot increase it by 10%. Try out a few encodes to see how it's responding and modify the threshold to what works best for your case. If you're using GKnot then you won't have the option of changing the threshold. Only when you use VirtualDub will you have full control over all the features.