I've had this problem forever while playing Cosmoteer, sometimes sounds would just rip my ears apart on 1/2 or 1/4th speed and only recently I realized what the problem is.
Whatever mechanism you are using to shift sound on slower game speeds (so it's deeper) also makes the sounds punch up in volume creating a volume overload. You would either have to add a (volume) limiter to your sound processing or change up the algorithm on how to treat sounds.
Here's an example of the sound overloading being caught on video:
(Those are spinning nuke storages btw)
EDIT: oops wrong flair, can't change it myself unfortunately, if anyone can I would appreciate.