Tools fly-outs not working?

Compared to the original post, I am speaking to you from the future! But what that actually means is that I ran into the same symptoms in Mac OS 15 Sequoia on an M3 MBP, working in Adobe Illustrator 2025 and InDesign 2025 (the problem wasn't happening in Photoshop 2025.) Because of this discrepency, it definitely felt as if I should be looking outside of Adobe products.

The solution for me was that in my Mac dock, I had the apps Assigned to specific Desktops. (right-click on your App icon, select Options...) Once I changed them to "all Desktops" I was good to go.  

Or are you talking about the secondary Tools in the Toolbox?

Whether I use it with, or without, my Wacom Intuos Pro, the fly-out options do not work unless I simultaneously press Control on the keyboard first.

While it's good this works, it's very clunky. On previous macs I used to be able to select them with my pointer (be it mouse or pen).

What are you saying – that a simple press with the Brush Tool for example used to raise the contextual menu for you instead of actually brushing?

Or did you use the button on the pen?