Sometimes when looking through stained glass, the water source rendered incorrectly.
Before 13w42a the water source occasionally show a bright blue color like viewing from outside (the third picture). In 13w42a and later versions the water source sometimes disappear (the first picture).
Also confirmed in creative mode.
How to reproduce:
1. Select world seed: 8707954756559826592
2.Go to x=-105, y=71, z=1 and build two-block-high stained glass panes there (like the fifth picture)
3.Stand in front of the glass pane and face west (like the fourth picture). You can see the water at the northwest direction disappears.
I have no idea what exactly caused this glitch yet.
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Might be similar source of the problem as in MC-34658 (Mods: NOT duplicate, similar!)

Looks more like a dublicate of MC-34795 to me.

Cannot confim neither in 13w42b nor in 13w43a

Added reproducing method.

Cannot reproduce since there is no river at that coordinates with that seed.
(Overread the minus sign of the x coordinate)
Please create a new world, build the glass panes, place the player and ZIP or 7Z the world and attach it here.

Testing this, I can't reproduce it. However, I have seen this bug occur with Nether Portals in videos that initially came out when transparency was originally adjusted. Its cause isn't very consistent, though. Does a moderator recommend, if this is observed, to do the forced crash for logging purposes?

World save file attached.

Totally confirmed with the attached world.

Looks like fixed in 1.7.2

Fix confirmed.

i still see it happening in 1.7.2. the only thing that got fixed was the blinking. before 1.7.2 it was blinking like crazy, now it's just permanently visible.
only part of the lake glitches through the stained glass though, but it's always the exact same part.
http://i.imgur.com/vCBXM7d.png
for the record, my pc is intel i5 3330, geforce gts 450, 8 gb ram, win7 64 bit.
edit: figured it out. the glitch happens when the x/z coordinates cross zero. whenever the coordinate goes from negative to positive, the glitch appears. happens to both x and z coordinates.

attached a screenshot that shows the bug still happening in 1.7.2
it wasn't fixed, the status/resolution needs to be changed.

Should be properly fixed in the latest snapshot and the next full version, please reopen if not.

still happens in 28a. it doesn't happen often, but from time to time you can still see things out of order if they're on the positive end of x or z axis.
apparently it's mostly transparent things like water, slime blocks and such.
attached screenshot

Does it still affect 14w30c?

If it seems like a duplicate of MC-9553
But I cannot confirm this with the provided world

Well as far as I've played it looks fixed.
Thanks