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.
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.