This is most likely because the UI now auto-orders the frame levels of elements of a frame in an annoying way (useful to some, not all
)
I make my own custom buttons, not using the Blizzard action button template, and each time my buttons are created or updated via configuration, I have to reorder the elements like this -
button:SetFrameLevel(4)
button.iconframe:SetFrameLevel(2)
button.iconframecooldown:SetFrameLevel(3)
"iconframe" is a special frame I made to put the icon texture in and the cooldown model is a part of it.
Basically, you just need to ensure your cooldown model is above your icon texture in frame level. I do remember that right after Blizz made the change, my cooldowns disappeared as well.