I had some similar problems while working on the MT missions. If you work on a mission with two different FRED-exes the mission file can mix up, e.g. I completely destroyed one of the missions and had to restart with a backup version. On another mission, I worked only with the current 3.6.9. build, but background somehow didn't show up. I removed all suns, saved, restarted FRED, re-added the suns and it did work.
You should also try disabling all graphic features (except the JPG/TGA thingie if your background is one of those filetypes), perhaps one of those doesn't work correctly for you.