So this is just a quick little helper for people not too familar with editing DOSBOX configs. I loaded up GOG's version of this game, and it just doesn't sound good compared to how I remember it and run it. Here's what I'd recommend changing:
Open RESOURCE.CFG in GoG's "Betrayal at Krondor" directory. Use this:
soundDrv = SNDBLAST.DRV
mouseDrv = none
memoryDrv = none
joyDrv = none
minEMS = 1024
minCPU = 386
minDOS = 500
size = 15000
cd=yes
nonrotatingmap = 1
nonrotatingmap = 1
Open "dosboxBAK.conf" scroll through it and find and replace the following sections with the following (they're listed below in order, and should be easy to find):
language=
machine=svga_s3
captures=capture
memsize=32
core=auto
cycles=12000
cycleup=500
cycledown=20
nosound=false
rate=44100
blocksize=1024
prebuffer=5
sbtype=sb16
sbbase=220
irq=7
dma=1
hdma=5
mixer=true
oplmode=auto
oplrate=22050
***** for some reason spaces are being inserted in the the words "auto" and "blocksize" and "mixer" above. Just remove them after you copy/paste.
Doing that eliminates the constant choppy audio for me, and replaced the sound effects from the default to the Sound Blaster 16 ones, which are much, much better.
The GoG version still has a "clicking" sound when a CD track is loaded, not sure what causes that... it's not there at all when using a mounted image of the game. But at least now the GoG version is no longer choppy, and the speed isn't crazy!

Did you try the replacing the
output=overlay
setting with
output=ddraw
under the [sdl] section? For me, this helped with some sound issues that were caused by the graphics being rendered very slowly under the overlay mode.

Yes, I wasn't sure if I should include that, because I think that stuff probably varies from driver to driver, but unfortunately it doesn't help! Thanks for the suggestion.
I have a DOSBox shortcut for the CD version, and one for GoG's, and the settings are basically the same, the CD version plays with no click before a CD track loads, but GoG's version has a single click/pop before each cd track starts.
Anyway, even if you don't need to go editing the DOSBox config file, you should update the Krondor one, to use Soundblaster, because the sound effects are very weak/poor with whatever GoG pre-configures the game's installation to (I think it was Roland MT32)

I don't doubt that this was an improvement for you, but in case it was not already obvious to everyone else you should keep a backup of any files you change. Doing the above changes actually created a lot of choppiness (win7 / mini9 netbook).
The point is: your mileage may vary, so leave yourself the ability to undo any changes =)
(Although in saying that, the GOG installer is clever enough that if you just delete the files you changed and then rerun the installer, it will only replace the missing files)

Nice post, fixed my sound effect nicely :) thanks!!
F.

You should still try changing just the Krondor specific config if you can, and leave the dosbox one alone. The difference between the soundblaster effects and the RT32 ones is day and night. I can't tolerate the way it is by default with GoG, even just dragging stuff to the inventory sounds atrocious! :)
But yes, it's always faster to create a copy before changing stuff! At least it is simple enough to restore via GoG's installer, sorry to hear your didn't have any luck with the settings I use. I guess if you aren't sure, it takes literally 1/2 second to create copies just to test it out.
Maybe someone else will have ideas to tweak it further, but there's nothing to lose but a few minutes of your time, and over the course of a 60 hour game, that's really not all that much! :)
Edit: If I had to guess what section caused you trouble perhaps it's this one in particular:
core=auto
cycles=12000
cycleup=500
cycledown=20
Leaving that one out of the changes might help. You can probably decide if it's worth your trouble, because even with additional choppiness the sound effects should be noticeably higher quality (depending how picky you are) with the Sound Blaster config.

This helped me. Thanks!

This indeed solved sound stuttering issues for me. Thanks a lot!