Do HP regen runes affect all those new %hp regen items?

No, they don't. Giving yourself regen runes is just giving you bonus regen. Similar to how using AD runes won't affect how much damage your sheen proc does (since it uses -base- AD). The % items are based off of the base regen that you start with / gain through levels.

good question

I don't know, but I'm very curious about the mana regen in the same way.

The documentation seem pretty bad at the moment, I think runes now give 10% health regen for every hp5 it was giving in the past. It doesnt seem to affect the base hp5 regen and multiply with in game items.

someone play and test it Out!!

I was wrong, the runes simply seem to add to your mana/health regen but not to your base regen.

If you have 10 base hp5, 150% regen and 10hp from runes you'll have 10*(1+1.5) + 10 = 35hp5