Next time, try worldedit's fixwater command. It will fix non-flat water and I think it also triggers flowing properly. There is also a fixlava, should you ever want to do that.

See how that works for you
http://dl.dropbox.com/u/24408505/world.zip

Here's a mediafire link: http://www.mediafire.com/?cv8avbddm4v9f2b

maybe, I've never tried to attach a world file here before. Probably have to zip it or rar it first.

Sure, if you want to upload it somewhere (mediafire or whetever you like) and send me a link I take a look at it see if I can fix it

ML32, could i just send you the map and have you try and fix it yourself? :0 Cuz i obviously cant manage to haha

hmm... I've never seen that before.

I suspect it's a glitch related to the water blocks placed with MCEdit. In that case, I would follow the same steps as above accept, instead of //set 8 i'd use //set 0 (air) or //cut. Once all the weird water is removed you can then type //set 8 and it should do the trick.

Ahh, I see.. then what is set8?

I never used world edit. But when ML32 said //pos1, //pos2, //set 8, do you think you should try //pos1, //pos1, //set8?

My (failed)logic: the pos2 is going by every other block instead of the block beside it.

It makes sense in my head, but my head hasn't worked correctly for a good while.

I'll admit.. that looks wicked! xD

This is the result that world edit gives me:[attachment=0]<attachment unavailable>[/attachment]

Yup that's the one. It's got single player support too. I would just make the area selection where you want the water (basically the same area you were trying with MCEdit) then set it to water blocks and watch it fall and fill in. It would go something like this:

//pos1, //pos2, //set 8
(there's probably other ways to do it too)

Have you tried the same situation with World Edit? That's what I use, works like a charm

I've tried pretty much everything i can think of, and nothing is working

With McEdit, try placing a lair of dirt on the 2nd to highest layer, then put the active water layer on top of that layer (which will be level to the water that's already around it).
Then get in there and dig out the dirt and see if that does anything.

Okay well i have removed the layer of water i placed over the dome in an attempt to clear it up. Heres a picture showing what the situation looks like right now.[attachment=0]<attachment unavailable>[/attachment] When I place a single layer of active(or stationary) water over the empty part over the dome, it doesn't flow down.

Make sure when you select it, you aren't using Stationary water. just type water instead of the number...

Still doesn't flow correctly

Try placing a block around the edge somewhere where a piece of non-falling water is. It might trigger the water to fall then.

I was originally gonna suggest that you just replace the air blocks with water blocks, but then you'd have water in your dome, lol

I just saw a picture of some dirt that is right beside the water. Dig that out and see if it does anything.