Edited: Oh, Ashley's reply has just disappeared so most of this won't make sense now!
Thanks for the reply Ashley, I appreciate it might be a niche issue. I can very easily reproduce it so if you want me to attach screenshots or anything just let me know.
I wonder if it 'thinks' the middle of the screen is higher up than it really is because of the scaling of the lower screen then? How does it determine the 'center' of the screen, is it percentage based based on the whole of the extended desktop or does it measure in pixels?
I've tried it with the App installed in Chrome too just now and it exhibits the same behavior.
I think most people use dual screens side by side, I use my vertically both at work and at home (I'm not a dev, I'm a network engineer by trade) that may be a factor, though it feels more like it's related to scaling. I will arrange (logically) side-by-side and test.
I have found the settings in the C3 menu and can use a new tab as a workaround but I'd prefer the popup window to work if possible. It wasn't an issue in C2.