I have this exact same problem, too, although it only seems to happen with certain mods installed. I found out which mods I could install and which once I could not, and the number of mods that I could not install made this a truly depressing thing.
I always first notice this during the initial cutscene at the start of the game just outside of Candlekeep. I used the cutscene as my tester for which mods would work and which ones would not. If the cutscene ran smooth, the mod was ok. If it got choppy, it was not at all ok and had to be uninstalled. Once uninstalled, the problem went away again.
I will try the ambient sound fix and hope it works. I will report back if I become able to use all the mods that I found problematic.
Edit: Turning off ambient sounds seems to have done the trick, now how does one use NearInfinity to extract the SFXSound.bif into the override folder? I cannot seem to find an option for doing so. It would be nice to have the sounds back. Perhaps someone can create some sort of special tool that will do that for us automatically, in the future. Also, I found two SFXSound.bif files, one in the "data" folder and the other in the bg1data folder. I wonder which one is the problem file? If I can figure out how to do it, I will just extract both into the override folder for now.
Edit2: Even though I couldn't seem to find the SFXSound.bif files in the Chitin.key via NearInfinity, I could find them using WinBiff made by TeamBG. Still, extracting them into the Override folder didn't seem to help the problem.
I wonder if there is a way to force the game to access the extracted sounds Vs. the ones archived in the .BIF files.
Edit3: I tried just deleting the SFXSound.bif entries from the CHITIN.KEY and found that I still had the problem, with the ambient sounds turned on. Frustrating.