Try using some kind of polish designed for minimizing small scratches on plastic. These usually have a bit of wax in them that fills the fine surface imperfections and shines up when you buff it.
It sounds to me like what is called a "short finish" in the industry. Essentially, if the glass is not produced by being simply floated out on a pool of molten tin, it may have gone through grind and polish steps. Sometimes, a grind step isn't performed long enough to get rid of the coarser grind performed previously, so the polish step can't overcome the residual surface damage.
If it isn't ground and polished, then it's possible that when it was tempered, it was put into the oven dirty. If that's the case, it's likely that the dirt has now permanently altered the surface. It could literally have a zillion tiny concave impressions that are acting like little lenses that magnify the dot grid of the CRT in those spots. This would give you the weird color sparkle you mentioned. It would only give you that effect with a monitor, and would probably be mostly imperceptible with anything else.
Does it change if you flip the glass front to back?
RandyT