1. Restart game
2. Login
3. Don't target anyone or anything, and immediately cast a spell which should put a buff on yourself (e.g., Evasion)
4. Portrait shows cooldown timer but no spell icon

I was able to fix this issue by changing the following line

to

  frame:SetFrameLevel(parent:GetFrameLevel() + 1)

I don't really know enough about WoW widgets to comment as to why this resolves it. My best guess is that the portrait frame and the icon frame are having the same frame level within a shared parent, which means that the last one set will take priority. Maybe the player frame updates changed which events caused the frame level to be set.

issue #429 is also related

Ryeshots comment fixed this exact issue i posted a few weeks back, changed 1 line in the txt file and works