Did you actually replace the thermal paste before? Or did you just put the heatsink back on with the paste that was already on it? If you take the heatsink off, the thermal paste is ruined and absolutely must be replaced. This is especially true with wax paste. If you try to use the heatsink without any paste at all, it is absolutely useless (almost no heat transfers). You need some good quality, fresh paste between the chip and the heatsink.
On the X58A-UD3R, there are many lights. The ones by the CPU, in order from lowest to highest, are:
1: Green - CPU temp above 60 C
2: Red - CPU temp above 70 C (manual says 80C but from my readings it is definitely 70)
3: Green - CPU voltage slightly high
4: Yellow- CPU voltage moderately high
5: Red - CPU voltage very high
The lights light up like a bar graph, so if both 1 and 2 are on that just means it is above 70C (and also above 60C), same goes for the voltage, the lower lights stay on when the higher ones come on
I have noticed that the temperature lights can "crash" in that resetting the PC while the temp lights are on will cause them to stay on until the temp gets high enough to flash them or turn them on again, they will shut off only when the temperature drops below the threshold again. This is probably why the green light is still on while you are at 48C, try heating up the PC with a burn test or something then cooling it down, the light should shut off.
