Stained glass is rendered in front of clouds when above cloud level.
At y<126 they look normal
At y>127 they seem to be in/in front of the glass
Steps:
1. Load a new World
2. Build up a 1x1 tower of stained glass to the maximum height
3. Open up Debug Screen to see where you are
4. Look at the clouds and constantly fly up until they change
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Can confirm.

Same thing happens with nether portal blocks

Confirmed. Does not affect normal glass or opaque blocks.

Yep, happens with all transparent blocks. Seems that there's an issue with the rendering order of clouds/transparent textures when you are the same height or above the clouds (more or less the same as MC-9553). Doesn't happen when you're underside the clouds because the bottom of clouds is not transparent (MC-997).
I would change the title of the ticket to "Transparent textures render behind clouds" to make it easier to find and mention in the description that this doesn't happen underside the clouds because of MC-997.
EDIT:
Generalized the title and description of MC-9553 so this can be closed as a dublicate of it.