This may be a known bug when you hear the SE from select, menu and save while playing in-game. The problem isn't the audio files, but it is the code written in Script Editor when the audio is played in-game. For some reason, the speed or frequency seems to have degrade sound quality, giving this crystal-like sounds. I tried comparing scripts v16.2 with v17.2, but I don't know where exactly to look. I did, however, check if .wav had any changes or if there's a problem within the compiler. I hope this isn't a .dll problem.
Got any ideas on how to correct the sound quality?
EDIT: In addition, inside the SE folder, .ogg files have also been degraded, being unusually slow so that's part of the audio problems.