This may be the case that you have picked up a quest like the one that (for example) says go and meet such and such at Brill. This will phase you or other quests for the Dragon Isles or The War Within will phase you until you complete the Silithus part.
It’s a major problem in the game right now. It stops people from skipping the MaW and getting the Quests in SW and Org from Darion to get to Oribos. I figured out the solution. Put it on here, but no acknowledgment from Blizzard like thanks for the help. Yes, I did get some help with people getting from Darion (like on Wowhead). But the hard part was getting to there. That took me a few days to work out. I lost precious time on the Celebration anniversary, getting the portal part of those quest done. Figured it out after. But since I didn’t get it done or hand in the other two quests I had in my log completed whilst this was happening. I dont get credit and don’t get the rest of the achievement, and can’t talk to Alyx to get the bike quest.
Even with help Blizzard, cleaning up their mess and telling them what the problem is. If they actually listened. It was under ‘Alyx, Alyx, who the Portal is Alyx’. Playing on the Smokie Alice song, and the trouble with portals. Which, incidently, comes back to your problem as well. It’s not a portal problem. It’s a phasing issue. even though I didn’t mention in that post, that’s what it comes down too. Some quests currently with this expansion, just don’t like sitting on tops of each other. Go, back see what quests are in you log. Maybe the Brill Calliel I think her name is (sorry sometimes I am good with names other times I am not. Finish the Brill intro. Finish the War Within Intro in Silithus. Finish the Dragon Isle Intro. These main intros first. Then some others will appear like the water one. Sorry I am forgetting names because of my disability. Though, I have survived helping in this post to get you where you need to be. With this, you may also see Darion in SW for MaW/Oribos. If you have done it previously you will be taken to Oribos and asked if you would like to skip and follow instructions etc.
Hopefully, I havent reposted something that someone already has. They may post the Darion stuff, but not many know about the other stuff, as I said I had to firgure it out, as there was nothing about it. Also, any intro stuff you do will give you experience. It will be higher the more closer it is to the current expac it is. Hopefully, I have helped you also, in part or full. Because that’s part of my values either seen or unseen. Happy adventuring! 
Here is the other post bout Alyx and Portals (now Phasing as well) - edited