Sorry if this is in the wrong spot, the intro page said to report PvP.net bugs here.
The basic issue is that for the Runes modified in the latest patch to enhance their stats (which may be all of them), the mouse-over tooltip does not reflect that enhancement while other portions of the GUI do. Here is an example:
In the Rune Combiner, we see that the Greater Quintessence of Warding gives +4.7 Magic Resist. However, the mouse over of it says that it is still giving the old value of +3.68 Magic Resist.
Rune Combination Bug-4-1.jpg
When you go look at the Rune in the Rune Book, we see that the calculated value for that Rune actually matches the Rune Combiner at +4.7 while the tooltip is still the incorrect +3.68.
Rune Combination Bug-4-2.jpg
This seems to affect most Runes as far as I can tell.