I'm always on Rune, but the only settings I changed was removed the first anti lag setting(on both) for quicker response... I tried your old version and stays at 90-100% mana all the time :< so I dunno why both versions act differently - ok so compared the logs for 2 fights and both had 91% uptime for rune,.
The Arcane rotation hasn't changed - other than Arcane Missles can now cast if you don't have Arcane Power to auto cast. If you've got it enabled (i.e. Boss/Player) then it's exactly the same.
Mana low -> As long as you don't run out then it's not an issue.