Well, first the obvious: does the background layer have transparency? I am not questioning if the background opacity and fill is at 100%, I am asking if the background layer has transparency. You could check this by creating a solid color layer and then duplicating the background layer and moving it over the dupe. Does color show through?
Second obvious question: did you perhaps activate a blend mode by accident? Some blend modes like Lighten and Darken could give the impression of partial transparency.
If those are not the problems, I would maybe start thinking that you may have one of those weird OpenGL/video card glitches. Try turning off the OpenGL Drawing in Edit>Preferences>Performance. If that fixes it but you want to try to keep the OpenGL functionality, check to see if there is an updated driver for your video card. That might help.
