Well... i did not do anything like that.
And i don't think this would explain the described behaviour.
Wouldn't always-on-top also affect the software rendered version?
And i am not talking about independant popup windows which the operating system is aware of.
Combo box drop down menu doesn't open and tooltips ain't shown anymore.
A completely new JUCE application with the default auto-generated MainWindow and a single combo box is already enough.
Add an OpenGLContext to MainWindow and activate Kiosk Mode and suddenly the combo box drop down won't work anymore.
At least on my system... I don't know whether this happens everywhere.
Just tested it on another Windows Notebook with the same results.
So this is definitely reproducible.