It depends on what type of VPN you have as well, because if you have one that gives you a dedicated IP, chances are it wouldn't be detected. But most of your regular cheap VPN packages will have you sharing the same IP as hundreds (thousands?) of others.
Good question. A lot of banks in Europe use this type of setup, where it will ask you for 3-4 characters of your pin/password, both to login and to confirm transactions. I always thought it was weird but never thought about the security implications.