There's an odd issue that came up in a modpack I've been helping to test for 1.9. When I have SciAPI and Stellar Sky installed, the Ender Dragon's health does not update and respawns after a certain amount of time when killed. It also doesn't spawn a the End portal blocks or the Ender Dragon eggs.

Environment:
MC 1.9
Forge 12.16.0.1811
SciAPI 1.3.0.3
Stellar Sky 0.3.2.2 and 0.3.1.3

Steps to repro:
Create new world and go into creative
Create an end portal and go to the end
Kill the Ender Dragon

I was using this command /give @p minecraft:diamond_sword 1 0 {ench:[{id:16,lvl:2000}]} to give myself a sharpness 2000 sword to kill the Ender Dragon in one hit to test this. I think Forge/MCP is still in flux so I'm guessing you might not get to this immediately but since I saw it still existed in the latest release I thought it was worth filing. I've only tested two versions of Stellar Sky, the one in the pack and the latest release.

How did you created end portal? Did you find just an existing one, or did you create a new one?

I just created a new end portal by using the frames you can place from creative. Hopefully that doesn't cause any side effects but that was how I was testing it.

Sorry I misunderstood. The directionality of the end frames does matter and they all have to be facing inwards to create the portal. I typically would place them from a single point, right in the middle of the portal I'm creating. Here's an imgur album http://imgur.com/a/CikzJ. Through the course of documenting this I think there might even be an easier way than creating a portal. You can use /setblock ~ ~ ~ minecraft:end_portal to set the block you are in to an end portal. It won't be a proper 3x3 but it still works. I would still recommend going into creative though.

Since im not ne able to create one.. please demonstrate your setup.

Thanks tested and it works great :)