What questions are you getting? For upgrade, you should only get License Agreement and the choice between full upgrade and custom upgrade.
https://winscp.net/eng/docs/ui_installer_license
https://winscp.net/eng/docs/ui_installer_setuptype

Just updated and it's a full reinstall, asking me all the first time install questions.

Would be preferable if it could "just update" without needing to ask me zillions of questions. Fair enough if there are new features, but if not then please minimise user interaction. Updates need to be as simple as possible.