I explored and mapped out all the nearest outer end islands encircling the main island before spawning in all 20 End Gateway Portals. I've now defeated the dragon 20 times but the portals generated on the main island AFTER I explored all the outer islands don't work. The enderpearl teleports you within the end gateway block and you suffocate with your head trapped in the bedrock above.
I've since re-explored the areas in the outer end islands corresponding to the broken portals, where the destination portals and their small islands should be and they haven't generated at all.
I guess this is because I had already generated that area before the destination portal was unlocked thus blocking its generation and breaking the original portal.
I hope you can find a bug fix or workaround!