I've done the horator thing, and the nerevarine?

When I go and talk to Saryoni he dismiss's me without hearing me at all. He just says goodbye, and I cant choose any dialogue.

I came in the secret door, if that means anything?

note; wow a fickle game. I just walked around in front of him and he started chatting me up.

You mean his voiced greeting message kicked in, or you actually got him to start his dialogue?

Here's the quest: http://www.uesp.net/wiki/Morrowind:Hortator_and_Nerevarine , check if you've done everything properly so far. Say, it is possible that you must talk to Danso Indules in order to engage dialogue with Saryoni, but I'm not sure.

One thing though, do you remember if you have gone to Saryoni's room before? And possibly taunted him angry or done some terrible crimes against the Temple in general? Check if he has high enough disposition with you to talk to you; it should be something like 20/100 at the very least, but it's likely even more.

You might have a disease. Some people won't talk to you if you're diseased or blighted.

This drops their Disposition, and a low Disposition can get you the instant "Goodbye" sometimes.