How does stacking/non-stacking work?

Let's take this very clear example: I had 506 health on my character and decided to replace a rune of vitae with a rune of major vigour. After my calculations, this would leave me with 537, but it did not. I was left with 496, since I replaced the +10 from the rune of vitae.

Why did the rune of major vigor not increase my health? I know it's non-stacking, but to my understanding, it would not have stacked if there was another bonus of the same kind on the same item.

Note that I have another rune of major vigor on another piece of armor that did increase my total health, but the second did not.

Which makes sense, but why then, do two +1(Non-stacking) Fire Magic, on different armor pieces add up to 2 attribute points?

Thanks for clarification.

They don't. I suspect you're thinking about the inherent +1 of a headpiece and a +1 given by a rune. So, if you have 1,2, or 5 +1 Fire Magic runes, you'll have a +1 (stacking) on your headpiece and +1 (non-stacking) from the runes. You'll often see this written as: Fire Magic 10+1+1.

You're right. And now it all makes sense. Thanks!

Runes of the same name, with the exception of attunement and vitae, do not stack with each other. You said you already had a major vigor, which adds +41 health, non stacking. And then you tried adding a minor vigor to replace a vitae rune. Since you applied 2 runes of the same name (vigor), the larger rune cancels out the smaller one (you get the +41 and not the +30). Since you replaced a vitae to do this, you lost the +10 health from the vitae that you replaced. The non-stacking clause applies to ALL of the armor you're currently wearing; you can't have more than one rune and one insignia on any piece of armor. So, if you wear a major vigor rune on one piece of armor, and then equip another piece that has a different vigor rune, the larger one will cancel the smaller one.

aodhan already explained the +1+1 thing, so I'll leave it at that.

Also, you should be aware that while bonuses of runes don't stack, the health losses will.

For example, if you use 2 superior fire runes you only get +3 fire (because the bonuses don't stack), but you will get -150hp (because the health losses do stack).