Custom Soundfont Unwanted Note Echoing/Fluttering

I'm trying to transcribe music using a custom soundfont. Most of the instruments work perfectly with this soundfont, but for specific instruments like flute and bass guitars, the notes echo/flutter either when clicked in note select or during playback regardless of note length. Note that the flutter frequency increases with the note's pitch. I'm new to audio design and unfamiliar with jargon/terminology, so I attached audio samples of what's happening. My goal is to edit these instruments so that they can play long continuous notes without fluttering (for instruments like the pan flute) or just play short, staccatoed notes without the echo (for bass guitar). How would I go about doing this? Feel free to define terms and jargon if it makes it easier to explain things.