I went back and reloaded the instrument in Logic, and this time I waited for the entire "preview" to load. I normally don't have to do this in standalone mode, because it happens much faster. The results were the same, but I did discover something interesting...
I loaded Noire, a Native Instruments sampled Piano library. It has particle effects to create unique sounds, and these particle effects are displayed within the instrument as ripples on the GUI panel. The sound is also off (similarly to Keyscape), but I noticed that the particle ripples are moving MUCH faster than they should be. It's almost like the PITCH of the instrument is what is being changed, because everything is somehow being sped up in Logic. I have no idea why this could be, but it makes sense that this would be causing the sound issues I have, because it does sound like the pitch is higher and more metallic. Running the Kontact Player outside of Logic runs the Noire Instrument fine, and the particles move at the normal speed.
I have no idea how this could be. Since Native Instruments is a completely different corporation than Keyscape, I'm beginning to think that it is Logic that is altering this somehow (and it could, of course, totally be my fault).