On my Linux machine (Gentoo Linux with libSDL 1.2.11) I noticed the following symptoms with the CVS version of VBA.
(a) Both SDL and GTK+ versions run much faster than 100% speed when they shouldn't. (The Windows version runs close to 100% speed when there is no throttle value set.)
(b) There are lots of sound stutters with both versions.
(c) The SDL version freezes with SDL_CloseAudio().
It seems to me that (a) is due to lack of syncing between the two threads [main/audio], and (b) is due to SDL_CondWait() in the callback functions. I rewrote some parts of the sound code and all the three symptoms seem to have disappeared on my machine. Unfortunately I have no additional machine to test it on, but I hope this be of help to somebody who suffers from the same problems.