I don't have this issue all that often but when I do it's the exact opposite problem (no light-side missions available, only dark-side). My assumption, and I think I'm correct in this, is that it's because you're "using up" (so to speak) the missions that you want, leaving the ones that you don't want sitting there. When it happened to me prior to Light V I would do a mission from another level that I needed or just wait a bit. Now it doesn't matter so I do all sorts of dark side missions (scandalous!).