To reproduce:
1. Open attached project "PNGImport.zip"
2. Open "New Scene" scene.
3. Drag "cloud 1" and "Tester0" Sprites into the scene.
4. Change both of their "Alpha is Transparent" setting to be unchecked, and then back to checked.
5. "cloud 1" is now always not transparent, "Tester0" is always transparent (as it was).

Expected result: if "Alpha is Transparent" is checked, then alpha channel is transparent, otherwise it's not.
Actual result: since 5.5.2p1 alpha channel is always not transparent, for "could 1" Sprite.

Reproducible: 5.5.2p1, 5.5.2p4, 5.6.0f2, 2017.1.0a4
Not reproducible: 5.5.2f1

Notes:
It happens only when .png is saved as an 8-bit file with transparency.
For example, in Photoshop, when exporting a .png you can checkmark the 8-bit file option.