I saw an answer to a similar post saying that you have to use .CUE files, and that is the extent of their fix. I know this is discussed more on the XBMP forums.
On another note, I also heard talk of XBMC implimenting a crossfader, and hopefully remove that silence or annoying pop/sound between tracks. I think i only notice the pop inbetween songs it since it's heavily amplified in my truck..