Hi StrangeBrewInTheNorth,
Thanks for contacting the Apple Support Communities!
We understand that when you download items using Safari, it defaults to the download folder rather than asking where you'd like to save the download as you've chosen.
To help isolate this behavior further, do you experience the same behavior if you create a new user account and change your Safari Preferences to ask you where you'd like to download your files?
To create a new user account, you can go to the Apple menu > System Preferences, then click Users & Groups.
Click the lock icon, then enter an administrator name and password.
Click the add button (+) below the list of users.
Complete the fields shown for an Administrator account, then click Create Account (or OK).
Once you’ve created the new account, go to the Apple menu > Log Out, then log in with the new account and test Safari after adjusting your preferences.
Let us know how it goes.
Cheers!