stuboy: I had this exact problem - smooth sound for a minute or two then horrible stuttering.
I played around with dosboxTLE.conf for a while, trying vagabond's audio settings. The breakthrough came when I changed the CPU cycles "cycles=max" to a manual variable, rather than letting the program estimate it (very badly, it would seem). 30000 seemed to give very smooth performance for me, and works even on a netbook. Give it a try.
I've used Vagabond's config, however it didn't solve the sound issue.
Changing cycles=max to cycles=3000 solved it, but in return messed up the video (instead of stuttering sound, I had stuttering graphics and cursor).
I looked at the config file again and saw the line 'core=auto', so I've tried setting 'cycles=auto'. It worked - now the graphics and the sound is just fine.
So if someone still has the same problem and cycles=3000 don't work, try setting it to auto.