As reported by Morrolan, he set a child region inside a parent region and had build: allow on the child region, and while blocks can be placed, fluids cannot.

You mean emptying buckets?

Yes.
(Also, ignore my 'stretchted' username, 'Morrolan' was already taken ;) )

Edit: Ok, I've just spawned water & lava blocks and was able to place them fine. Seems it's really an issue with emptying buckets, should have made this clearer I guess.

Edit2: Also, the 'use' and 'water-flow' flags are both set to true.

Can't reproduce. Buckets are acting the same as breaking/placing any other block for me.

I see. Should be fixed now.

That's strange then, I just played around some more, but was always able to reproduce it:
I just set up a new local server with CommandBook, Worldedit and Worldguard only.
Then I've created a region and set the build flag to allow. No other flags or child/parent relationships are set
Then I've tried to place blocks, which worked fine.
And finally I've tried to empty a bucket inside that region, which did not work. It did not say that I don't have permission for this region, but it just disappeared. (The water, not the bucket)

Edit: Oh, I think we're getting closer.
The issue I describe happens in cauldrons only. Sorry that I didn't mention this here, that information must have got lost in the transfer IRC -> github.

Edit2: Getting stranger and stranger.
After placing some blocks and trying to place some water it suddendly starts working as it's supposed to. I'll try to reproduce it. :S

Edit3: Ok, everything's clear now, sorry for the confusion. ;)
The issue is not related to cauldrons. And the fact that it at first did not work, but later it does might just be the time it takes for the flag to start working.
The issue I had was this:
This is the cauldron I used to test it. Since it is not related to cauldrons the same result could be achieved with any other area: http://i.imgur.com/6jnek.jpg
There is a big region around this cauldron, which protects stuff around it.
Now since I wanted to allow people to use that cauldron I've set up a litle region inside the cauldron. This region is indicated with red wool here: http://i.imgur.com/VTdZw.jpg
Now when you try to empty a bucket inside the cauldron it somehow checks whether you may build on the block you rightclick with a bucket, and not whether you may build on the block the water would be placed. For illustrational purpose: If I were to empty a waterbucket where the orange block is (by right-clicking the yellow block with a bucket) it would check whether I have build rights for the yellow block, instead of checking for buildrights for the orange block. http://i.imgur.com/1GHiv.png
Now since the region I set up for the cauldron does not contain the yellow blocks emptying a waterbucket where the orange block is is not allowed.

So unless this behaviour is not intended but a bug this issue can be closed. Sorry for the confusion, should have played around some more first. :)