It looks like this:

The other icons show once I place my mouse somewhere within in the frame and they disappear a few seconds after I move the cursor out of the frame.

It's showing the following buttons: ItemRack, Gargul, Details, DBM, AtlasLoot, LFG Bulletin Board, WeakAuras, RestedXP, Questie, NovaWorldBuffs

The Icon that always shows is "LFG Bulleting Board"

Figured it out, it was Leatrix Plus attempting to hide them except on mouseover of the minimap, thanks!

Not sure why LFG Bulletin Board behaved differently, it works correctly with MinimapButtonButton disabled but whatever

Could you temporarily disable MinimapButtonButton and see if the icons still disappear until you mouse over them?
My suspision is that some other addon is adding the "show on hover only" behaviour as MinimapButtonButton doesn't include such behaviour.
I could make a test build that blocks changing the alpha of collected buttons as the "show on hover" functionality works by making the buttons fully transparent.