I'm having exactly the same issue as the OP - and OP's original post (OP's O.P.?). Sega CD games with sound effects but no soundtrack. Using .cue/.bin files. RetroArch/Libretro forums are currently down, but if anyone can shed some light that would be slick.
EDIT: Well, not EXACTLY the same problem. I get sound effects, but no "CD Audio". That is background music, etc. .CUE files all look correct and .bin files are all present.