The issue evolved somewhat in full release, now the pane isn't rendered in front of the portal, but viewed through the portal it renders over it. Looking from positive to negative axis renders properly though. Also the flickering is gone, making it easier to reproduce.
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If you view a nether portal on negative X axis through stained glass (pane or block) on positive X axis it doesn't always render, Same is true for vice versa and Y axis. It's a bit fickle to reproduce because from many angles and distances it renders properly.
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This actually occurs across every multiple of X=1024 and Z=1024 (0, +/-1024, +/-2048, etc.) and with all semi-transparent blocks against water or portals. The visible direction depends on where you are:
West of x=0 and at x=0 , the glitch is visible from the west when looking at north-south lines.
East of x=0, the glitch is visible from the east.
North of z=0 and at z=0, the glitch is visible from the north when looking at east-west lines.
South of z=0, the glitch is visible from the south.
Here's a series of test images taken on a modified Waterworld superflat preset. A 6x6 base is placed with its center at x=1024,z=1024, followed by a ring around the outside of the next layer. Water is placed in the 4x4 center cavity then covered with another layer of ice. Each shot is taken from one of the corners of the structure facing the opposite corner.
Preset code: 2;7,5x1,5x3,5x12,90x9,79;12
Ezekiel
Fixed. citation
Yep, fixed. All sides look like the NW Corner pic above, like they should.
Hmm. Now when I go under the ice and look up through the water, there are similar glitches visible at certain angles on various blocks. I haven't figured out the pattern yet, but I'll probably open a new issue once I do...