I keep doing that too.
LOL for me it gets worse, some times I've clicked Preferences without paying attention to which one I was clicking, and then realised it was the wrong window, closed it, but then didn't remember which one I had clicked, because in my head I had clicked conceptually the correct menu item anyway (because "settings" and "preferences" mean the same thing), and then I clicked the wrong item yet again, this time paying attention. Now every time I need to get to either of these dialogs I think to myself "Alright, folks, we are clicking the top one, I repeat, THE TOP ONE, it's 50/50, let's go!" often followed by "Abort! Abort! It was the bottom one. Dang it!" As I type this I still can't remember which is which.
Realistically I hardly ever go into these menus. If I was tweaking this stuff every day I'd remember what's what and what's where. If there's reason keep them in two separate GUIs maybe RME could consider changing the menu item text to make it easier to remember; otherwise, merging them into the Settings window as tab would be even better.
The Preferences window is a bit taller than the Settings window because it contains a lot of settings, maybe that's the reason for keeping stuff separate, because it won't fit on a single tab of the Settings window. A scroll-able GUI would solve this problem as it would accommodate any number of parameters.
Fireface UCX II, BabyFace Pro, Fireface UFX, Fireface 400