I beat the ender dragon 3 times in my survival world and it never generated for me either. HOWEVER, I created a new world with the same seed as my survival world and went in creative mode this time I killed the ender dragon twice to test this and it turned out the End Gateways generated both times there. Really strange bug.
For anyone that needs a temporary solution, you can bridge about 1000 blocks in any direction from the main island to reach the Gateway islands. I did this in my survival world yesterday. It takes a while but you will get there if you have enough blocks. On the outer islands I did find a Gateway I could use to get back on the main island. The problem seems to only occur with the Gateways that appear after defeating the Ender Dragonn