OK, so it just got weirder.
I tried to record a sample audio to send you how it sounds. However, I found out that the problem is with the Duet's output. Because the audio I recorded sounded normal through the built-in output, but through the Duet's output it sounded as if there was a mild phaser or flanger effect, and as the sound sustains it starts to stutter mildly. It is quite difficult to describe but it sounds as if there is some sort of effect, which makes the sound more synth-like.
P.S. Sorry I posted this problem on a Logic forum, initially I thought it was a problem with the DAW settings. However, members of this forum are extremely knowledgable, so maybe someone will have an idea about the problem. I am sorry for the inconvenience, but thanks to your help, at least I was able to discover the source of the problem.